world class science, creating first class beef cooperative ...cj hawkins homestead, university of...
TRANSCRIPT
CJ Hawkins Homestead, University of New England, Armidale NSW 2351p 02 6773 3501 • f 02 6773 3500 • e [email protected] • w www.beefcrc.com.au
The Beef Cooperative Research Centre (Beef CRC) is Australia’s largest integrated beef research program bringing together leading beef researchers from across Australia along with prestigious national and international beef industry partners and biotechnology businesses.
The world class research underway by the Beef CRC aims to increase profits for Australia’s cattle industry by at least $179 million per annum from 2012.
To do this, the Beef CRC is focusing on gene discovery and gene expression which will create precision breeding and management strategies to improve profitability for all sectors of the Australian beef industry - breeding, growing, finishing, processing and retailing.
Aboutus
Rockhampton
Brisbane
Armidale (Beef CRC HQ)
Melbourne
AdelaidePerth
Wellington
Beef CRC Major Research Sites
Research StationsBelmont, Qld
Brian Pastures, QldBrigalow, Qld
Swans Lagoon, QldToorak, Qld
Glen Innes, NSWTrangie, NSW
Tullimba, NSWHamilton, Vic
Struan, SAVasse, WA
Contactus
Established and supported under the Australian Government’s Cooperative Research Centres Program
Cooperative Research Centre forBeef Genetic Technologies
ANNUALREPORT2005/2006
World class science, creating first class beef
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Core Participants
Supporting Participants
Mission
To capture the benefits of the human and bovine genome projects and the ‘Livestock Revolution’ by improving the profitability, productivity, animal welfare and responsible resource use of Australian and global beef businesses through world-class gene discovery and gene expression research and accelerated adoption of beef industry technologies.
Outcomes
The CRC for Beef Genetic Technologies is targeting an additional $179 million in gross revenue of the Australian beef industry from 2012 using emerging genetic technologies to:
• Improve capacity to deliver high quality beef to Australia’s 110 global markets using cattle of known genetic merit for exacting specifications without compromising animal welfare or the environment.
• Enhance beef yield and herd reproductive efficiency, improve efficiency of resource use, reduce production costs, minimise methane emissions and avoid chemical and antibiotic residues through precise application of knowledge about the genes controlling these attributes in cattle, their rumen microorganisms and in parasites that affect cattle productivity.
• Ensure Australia is the number one supplier of beef to meet the growing demand by neighbouring Asian countries to 2020.
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ANNUAL REPORT CONTENTS
Chairman’s Report & Executive Summary > 5 Governance, Structure & Management > ��
Context & Major Developments > �9 CRC for Cattle & Beef Quality (CRCII) > �5
Research Collaboration- CRCIII > 4� Education & Training > 57
Communication Strategy & Specified Personnel > 6�Publications > 67
Financial Report > 75 Glossary > 9�
Australia’s largestintegrated beef research program
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Chairman’s Report and Executive Summary
Mr Guy Fitzhardinge(Chairman)
Dr Heather Burrow(Chief Executive Officer)
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2005/06 was an exciting year for the new Beef CRC Board, faced with the great challenges of starting an incorporated company (Beef CRC Limited) from scratch, with an entirely new Board and Centre Management and developing very ambitious world-class research, development, education and commercialisation programs around the CRC’s new theme of “Gene Discovery, Gene Expression and Accelerated Adoption,” whilst at the same time oversighting the wind-up of CRCII research and ensuring delivery of outputs from that research to industry.
Our first challenge was to actually form the new CRC Company and CRC Board. The CRC for Beef Genetic Technologies commenced operations on 1 July 2005 and now operates as an incorporated company limited by guarantee (Beef CRC Ltd) under the control of a largely independent Board. Members of the Company are the nine Participants of the CRC for Beef Genetic Technologies.
A significant difference between the new CRC Board and the earlier CRC Boards is that we now have a smaller Board, comprising Directors elected only on the basis of the skills they can bring to the Beef CRC, and not on their ability to represent partner organisations as occurred in the past. Election of Directors required formation of a Nomination Committee, which I was very pleased to chair, and widespread advertisements seeking Expressions of Interest from potential Directors. From around 60 Expressions of Interest, a short-list was prepared and interviews conducted to decide the successful applicants. We were indeed very fortunate to secure the services of such high-calibre Directors as those described elsewhere in this report.
Unfortunately though, we were also very saddened to hear in late September 2005 of the sudden and unexpected death of Dr John Vercoe, one of the CRC’s recently-elected Directors. John had been involved in one way or another in previous Beef CRCs and their activities ever since the initial establishment phase in 1991-1992. John had a very strong history of collaboration and interaction with many of the CRC’s scientists, extension
staff and beef industry partners and was one of the drivers of the first successful Beef CRC bid that integrated Queensland as part of the CRC application. He was subsequently appointed as the CRC’s first Official Visitor. At the time of his death, the new Board had been very keenly anticipating John’s ongoing contributions and wise council in their deliberations. His inputs to the Beef CRC were always greatly appreciated and have since been very sadly missed.
Priority actions for the Board over the past year have included the development of policies for the full range of Board and CRC functions, consideration and approval of Year 1 (September 2005) and Year 2 (June 2006) budgets and development of a Board Charter to guide all the Board’s activities.
The CRC was officially launched at a high profile public event at the University of New England in December 2005 by Mr Hugh Morgan AC, immediate past president of the Business Council of Australia, former Chief Executive of Western Mining and an enthusiastic Hereford breeder from Victoria.
Another highlight for the Beef CRC came by way of an outstanding endorsement of the CRC’s work with Meat Standards Australia (MSA) by the Deputy Prime Minister and
Chairman’s Report(Mr Guy Fitzhardinge)
Hugh Morgan AC unveiling the plaque while Chairman Guy Fitzhardinge looks on at the launch of the Beef CRC
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Minister for Trade, the Hon. Mark Vaile MP at Beef Australia 2006 in Rockhampton in May 2006. During his presentation, the Deputy Prime Minister emphasised the very significant impact achieved by MSA (underpinned by Beef CRC science) on Australia’s economy. The independent economic impact study found MSA had delivered $244 million value-add for the cattle industry between 1999 and 2006. These net-of-adoption costs returned a value-add increase per research dollar in excess of $8 per $1 in research expenditure and contributed greatly to a significant finding from the study that
“… benefits delivered through the end user application of research by means other than direct commercialisation processes (spin-offs and licensing) remain the most significant channel of quantified benefits from the CRC Programme.”
This finding provides very strong support and credibility for the Board’s position of basing its strongest decision-making emphasis on accruing benefits for the Australian beef industry rather than returns from investment to CRC partners from Centre Intellectual Property.
It is very pleasing to report that by the end of June 2006, all research and commercialisation outputs from Year 7 of the
CRC for Cattle and Beef Quality had been achieved in line with the agreed milestones. Research outputs included several provisional patents for DNA tests associated with carcase and beef quality attributes and efficiency of feed utilisation.
As well, research, education and commercialisation/utilisation programs and projects in the CRC for Beef Genetic Technologies were also well on track, in accord with the milestones outlined in the Commonwealth Agreement. Early wins had been achieved by the new CRC from a Whole Genome Scan undertaken in Program 1, with a provisional patent lodged in Year 1 for gene markers for beef eating quality (Meat Standards Australia palatability score).
Finally, I would like to formally record my very sincere thanks and congratulations to the former CRC Chairman, Mr Peter Frawley and his very capable Board for their efforts and success in steering the CRC for Cattle and Beef Quality to achieve a third-term Beef CRC. I would also like to record special thanks to Professor Bernie Bindon for his efforts in establishing and leading the first and second phases of the Beef CRC and for so capably leading development of the third phase. The Australian beef industry is indebted to all of them for their efforts through the Beef CRC.
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The 2005/06 financial year has been an all-consuming period of activity for the reduced number of CRC headquarters staff and new CRC program managers, as they dealt with the overwhelming requirements of effectively administering and winding up CRCII Year 7 activities, simultaneously commencing CRCIII activities, seeking additional funds to support the new CRC’s very ambitious programs, establishing the new Beef CRC Ltd company and its new Board, employing key new personnel to undertake some of the necessary administrative functions (this need resulting from the decision to upgrade two key positions in the transition from CRCII to CRCIII and to appoint a new Deputy CEO), formally handing over the responsibility of CRC activities from the CRCII Board and the CRC’s foundation CEO to the new CRC Board and new CEO and introducing that new CRC Board to the vast complexities of the Beef CRC. It is with a great deal of pride that we are able to report that most of these activities were successfully achieved, although some important legal agreements were still to be finalised at 30 June 2006.
In addition to these critical administrative functions, CRC Management and Staff maintained a heavy schedule of partner and industry interactions and presentations and were responsible for the organisation and conduct several high-profile events including the official launch of the CRC for Beef Genetic Technologies, the “Australian Beef – The Leader!” conference and associated gala dinner to formally mark Professor Bernie Bindon’s retirement from the Beef CRC and a number of CRC activities at Beef Australia 2006.
In spite of these overwhelming activities, excellent progress has been made in effectively commencing the new Beef CRC’s world-class research, education and industry “adoption” and “awareness” strategies. This has required a major cultural change amongst the CRC’s scientific and industry extension staff, who
Highlights
• A smooth and effective transition was achieved from the CRC for Cattle and Beef Quality to the CRC for Beef Genetic Technologies, including major changes to the CRC Board, CRC Management and strategic directions of the new CRC.
• The CRC for Beef Genetic Technologies was successfully established and officially launched at a high profile public event in Armidale in December 2005.
• Beef CRC Ltd and its new skills-based Board were successfully formed and critical policies developed, documented and effectively implemented.
• Research and commercialisation outputs from the CRC for Cattle and Beef Quality were achieved in line with agreed milestones, including achievement of several provisional patents for DNA tests associated with carcase and beef quality attributes and efficiency of feed utilisation.
• Research, education and commercialisation / utilisation programs and projects in the CRC for Beef Genetic Technologies are well on track in accord with milestones outlined in the Commonwealth Agreement.
are now clearly targeting scientific and industry outcomes based on increased profitability and productivity goals in industry, reduced greenhouse gas emissions and improved animal welfare, rather than specific scientific outputs such as DNA tests, BREEDPLAN EBVs and non-genetic treatments. That these RD&E strategies have been so effectively established in such a short period of time and with such a major change of focus to industry outcomes is due to the genuine dedication and commitment of CRC staff across the entire CRC network.
Specific activities over 2005/2006 included the following.
Winding up the CRC for Cattle and Beef Quality
The CRC for Cattle and Beef Quality was formally terminated on 19th August 2005 by a Deed of Termination signed by the CRCII Core Partners and DEST. The CRCII Board met for the final time in Sydney in September 2005, to approve the Year 6 audit report.
CRCII Year 7 activities became the formal responsibility of the new CRC Board, using funds carried over from CRCII as well as $1m of CRC Commonwealth funds, now rolled into the Commonwealth’s $30m cash contribution to the new CRC. Operational Plans for Year 7 activities and their budgets were recommended to the new CRC Board as part of transition arrangements put in place by the CRCII Board.
Establishing Beef CRC Ltd
The CRC for Beef Genetic Technologies operates as an incorporated company (Beef CRC Ltd) under the control of a largely independent Board comprising an independent industry Chairman (Mr Guy Fitzhardinge), seven skills-based Directors (two Directors with experience in research
Executive Summary(Dr Heather Burrow)
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management – Professor David Siddle and Dr Keith Steele; two Directors with experience in beef industry issues – Mr Rob Backus and Mrs Lucinda Corrigan; and remaining Directors with specialist skills required by the Company e.g. management and commercialisation of IP – Dr Jay Hetzel and Professor Grant Sutherland; and knowledge of CRCs and CRC networks and the ability to interface IP commercialisation with industry uptake – the late Dr John Vercoe, replaced by Dr Greg Robbins in April 2006) and the Chief Executive Officer (Dr Heather Burrow) who is also Managing Director.
Members of the Company are the nine Participants of the CRC for Beef Genetic Technologies (DPI NSW; DPI&F Qld; DPI Victoria; Meat and Livestock Australia; Meat and Wool New Zealand; SARDI; University of Adelaide, UNE, University of Queensland).
Establishing the CRC for Beef Genetic Technologies
The Commonwealth and Participants’ Agreements were finalised in August 2005. A licence Agreement to license IP and materials from CRCI/II to CRCIII was finalised prior to 30 June 2006, but will be signed simultaneously to the CSIRO Supporting Participant’s Agreement. Supporting Participants’ Agreements have been finalised with Murdoch University, Department of Agriculture WA and Ohio State University.
The CRC Board approved Year 1 Project Details and Operational Plans at successive meetings in September and December 2005, with final approval for all Year 1 activities given at their February 2006 meeting. Year 2 Project Details and Operational Plans were approval by the Board in June 2006.
Over the past year, a number of important documents were developed by the Board, including a Board Charter; policies associated with Finance and Audit, CEO and Director Remuneration, Industry Impact and Adoption, and IP and Commercialisation; an operational level Policies and Procedures Manual; and Centre Communications Plan.
Official launch of the CRC for Beef Genetic Technologies
Mr Hugh Morgan AC, immediate past president of the Business Council of Australia, former Chief Executive of Western Mining and a Hereford breeder from Victoria, officially launched the CRC for Beef Genetic Technologies at UNE, Armidale on Tuesday 13 December 2005. In launching the new Beef CRC, Mr Morgan told the audience that it was hard to imagine a better investment of $30m of tax-payers’ money, given the potential benefits to Australia from increased export earnings, regional employment and prosperity and improvements in Australia’s national scientific capacity to be derived from the CRC for Beef
Genetic Technologies. Federal Member for New England, the Hon. Tony Windsor MP and UNE Pro-Vice Chancellor (Research) Professor Peter Flood also spoke briefly in support of the CRC.
Prior to the launch, invited guests enjoyed a sit-down steak meal, clearly demonstrating the proof of the beef is in the eating! Following the launch, attendees heard a brief overview about the foundations of the new Beef CRC (Bernie Bindon) and plans for the CRC for Beef Genetic Technologies (Heather Burrow, Mike Goddard, Dave Pethick, Wayne Pitchford, John Gibson, Jim Walkley, John Thompson and Jay Hetzel).L-R: Bryn Evans (DEST), Jennifer Gibb (DEST), Peter Flood (UNE), Ian Purvis (CSIRO) at the launch of the Beef CRC
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Staffing the new CRC’s headquarters
Considerable effort was required in Year 1 to fully staff the new CRC headquarters and establish HR procedures for the new company (in CRCI and II, all CRC headquarters staff were employed by partner organisations or the CRC’s Centre Agent, ABRI). Heather Burrow transferred to Armidale in early 2005 to prepare for the new CRC and to take up the role of Chief Executive from 1 July 2005. She is now a fulltime employee of Beef CRC Ltd. As a result of a decision to deliberately upgrade some CRCII positions, the key positions of Business Development and Finance Manager and Communications Manager were vacant at the start of the new CRC. Geoff Allen commenced duties as the CRC Business Development and Finance Manager (also incorporating the Beef CRC Ltd Chief Financial Officer and Company Secretary roles) in October 2005, coinciding with the transfer of existing CRC staff (Cynthia Mulholland and Susan Webeck) from ABRI to Beef CRC Ltd. Warwick Fraser commenced duties as the CRC’s Communication Manager in February 2006, at the same time as Paul Arthur formally commenced as the CRC’s Deputy Chief Executive. Paul remains an employee of NSW DPI, but has a commitment of 40% of his time as Deputy CEO and 10% research commitment within Program 2.
Research program quality and milestone achievement
The quality of the CRC’s portfolio (including progress to date and new Operational Plans and budgets aligned with the Commonwealth Agreement) is assessed by a combination of the CRC’s annual cycle of review, biennial independent scientific review and DEST-imposed external reviews after Years 1 (2007) and 3 (2009).
The CRC’s annual scientific and industry review is conducted by separate panels comprising CRC Management and partner organisations who undertake an annual peer review of the scientific merit and industry relevance of all CRC programs. Where required or desirable, specialist external advice is co-opted to the review panels to help assess particular aspects of the CRC’s portfolio. The review process also provides the partner organisations with an opportunity to undertake their own evaluation to ensure the CRC’s portfolio remains strongly aligned with the strategic direction of their own organisations (i.e. it provides them with the necessary opportunity to protect their investment in the CRC). In past CRCs, the partners’ Board representatives were responsible for maintaining alignment between the CRC and
its partners. But in the new CRC, the partner organisations no longer have Board representation. Hence, the annual review process now has even greater importance than in the past. The first scientific and industry review of the new CRC was undertaken in Armidale on 13 and 14 September 2005. The 2006 review occurred in Armidale from 19-21 April.
In addition to the annual reviews, the CRC Board has commissioned independent reviews of the science, focusing specifically on the technologies rather than the scientific and industry outcomes examined by the annual reviews. Hence, separate expert panels will be convened in 2006/2007 and thereafter at 18 month – 2 yearly intervals, specifically to review the areas of i) gene discovery, gene expression and RNAi; ii) microbial genomics and iii) adoption science.
To assist with ongoing project management, the CRC Board approved the purchase of an off-the-shelf project management software package known as “CRC Centric” to replace the existing manual and somewhat onerous spreadsheet- and email-based project management and information system. CRC reporting requirements continue to increase in complexity and there was a need to implement a more effective project management and information system.
Delegates at the Scientific and Industry Review
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“CRC Centric” is a web-based reporting system specifically designed by and for CRCs. The system includes functionality in many areas including program and project management by milestone and outcome; student and educational program management; effort (in-kind) reporting; IP register and tracking; comprehensive document management; reporting in standard formats; publications’ authorisation process; and secure (authorised) information online for all levels within the organization including Board, management, staff, students, auditors and reviewers. The system is very easy and intuitive to use and, available worldwide 24/7. It is effectively a secure intranet system for people working in the Beef CRC, with access to different levels of information through a password protected system. The system is milestone and outcome driven and therefore focuses attention on important issues.
The system has been populated with program and project information derived from the Commonwealth and Participants’ Agreements, Year 1 and 2 Operational Plans and budgets, Business Papers and minutes from a range of CRC Committees including the Board and its sub-committees, Beef CRC Ltd, Management Committee and its subcommittees and Centre Forum. Training staff in the use of the system has also occurred.
The impact of new genomic tools
The availability of new genomic tools such as whole genome scans (WGS) are speeding up discovery of QTL for a range of economically important traits. Results are now available from two whole genome scans that specifically targeted feed efficiency. Mike Goddard and his VDPI group used the Trangie Angus NFI lines for their WGS, while Bill Barendse and his CSIRO group used the CRCI steers measured for NFI for their WGS. Both groups are now validating results on promising QTL for net feed efficiency. Provisional patent applications were submitted by both teams.
Additional WGS have been completed in CRCIII Programs 1 and 4 to specifically target genes associated with meat quality and
female reproductive performance respectively. A provisional patent has been filed for associations with meat eating quality (MSA MQ4 score) in Program 1.
The CRC Board recently approved funds to allow inclusion of Bos indicus SNP (single nucleotide polymorphisms) in the chips used for whole genome scanning. This initiative is being jointly funded by Beef CRC, the International Livestock Research Institute in Kenya and EMBRAPA in Brazil. Development of a 32K SNP chip that includes SNP derived from Bos indicus will have a significant impact on the CRC’s future research, as several CRC cattle resource populations are based on Bos indicus or indicine-derived animals. Work is also underway to genotype all CRCI and CRCII animals for commercially available GeneStar tests to provide data to deliver a marker-assisted EBV model for BREEDPLAN developed by AGBU. A grant received from the Queensland Department of State Development and Innovation is assisting this research.
Education and Training activities
The aim of the CRC’s Education and Training Program is to deliver a more skilled beef industry workforce resulting from postgraduate, undergraduate and vocational training in the sciences underpinning beef genetic improvement and commercialisation and adoption of outcomes by the beef industry.
Eleven post-graduate scholarships were awarded in December 2005. The milestone was to achieve 7 new postgraduate students by June 2006, but given the calibre of the first intake, 11 places were offered. Since then, another 5 students have commenced postgraduate research in the Beef CRC’s program.
Eleven summer scholarships were also awarded to Honours Year students in December 2005 as an initiative to encourage students to enter a career in science and the beef industry.
Significant efforts were made over the past year to summarise and deliver outputs from the CRC for Cattle and Beef Quality in educational and information packages aimed at
Members of a Western Australian Beef Profit Partnership
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generating “awareness” of the CRC’s research, education and commercialisation / utilisation activities, including updating and upgrading the CRC web site and further developing and officially launching the “Livestock Library” in conjunction with the Australian Sheep Industry CRC and Australian Wool Innovation.
The CRC’s Education and Training Program also initiated a major change in the approach being used to achieve uptake of technologies by beef industry end-users. The new approach required a genuine cultural change amongst the CRC’s research and extension staff, a major feat in its own right. CRC staff are now very clearly and positively targeting scientific and industry outcomes based on industry profitability, productivity, greenhouse gas emissions and animal welfare, rather than specific research outputs such as genetic and non genetic products, number of patents and scientific papers etc. At 30 June 2006, about 50 “Beef Profit Partnerships” had been identified across all states of Australia and New Zealand, including 5 supply chains involving innovative meat processing businesses. Several partnerships have already commenced their initial benchmarking efforts using the CRC’s industry profitability framework against which progress towards achievement of profitability- and productivity-based outcomes will be monitored, measured and reported twice per year over the life of the CRC.
“Australian Beef – The Leader!” Conference
The “Australian Beef – The Leader!” Conference was conducted to showcase the results of two phases of Beef CRC research, co-funded through CRC Commonwealth and MLA funds, including world class scientific research carried out between 1993 and 2005. Presenters included a wide range of Australian and international scientists and beef industry professionals. More than 300 people representing all sectors of the Australian and international cattle industry attended the conference in Armidale on 7 and 8 March 2006, with delegates travelling from throughout Australia as well as from the USA, England, Ireland, Korea and New Zealand.
The conference also coincided with the formal retirement of Professor Bernie Bindon after a very long and successful career in livestock research and research management. In commemoration of this, a “Festschrift” in the form of a Special Edition of the AJEA and a Conference Proceedings showcasing the Beef CRC’s achievements under Bernie’s leadership were released for the first time at the conference. In addition, a gala testimonial dinner was held in conjunction with the conference to formally acknowledge Bernie’s contributions to science and the Australian livestock industries.
Beef Australia �006 and World Meat Congress
The Beef CRC was well represented at the Australian beef industry’s triennial
exposition, Beef Australia 2006 in Rockhampton in May 2006. The CRC hosted two Beef CRC seminars, the second of which included a formal presentation by the Deputy Prime Minister and Minister for Trade, the Hon. Mark Vaile MP. Beef CRC also participated in a “Showcasing Beef Genetics” seminar chaired by the Minister for Agriculture, Forestry and Fisheries, the Hon. Peter McGauran MP, MLA’s Meat Profit Day held in conjunction with Beef 2006, as well as manning an information booth in the QDPI&F pavilion. The CRC was also represented through keynote presentations at the World Meat Congress held in Brisbane the previous week.
During his presentation, the Deputy Prime Minister announced results from the first economic evaluation of Meat Standards Australia, a grading system designed and created by the Australian beef industry through Meat and Livestock Australia and underpinned by Beef CRC science. The study found MSA had delivered $244 million for the cattle industry between 1999 and 2006.
Announcing the results, Minister Vaile said he and the coalition government were proud to be a part of the world class research underway by Beef CRC. “Australia is regarded as world leader in beef technology innovation,” the Deputy Prime Minister said, “and it is a reputation enhanced by the work of the Beef CRC proudly supported by the Government of which I am a part.”
CRC Association Conference
The economic impact of Meat Standards Australia, underpinned by Beef CRC science, was also highlighted by MSA Program Manager Mr Allan Bloxsom at the CRC Association conference in Brisbane in May 2006. The MSA presentation was followed by an end user perspective on Beef CRC technologies, presented by CEO of the Australian Agricultural Company (AACo), Mr Don Mackay. Mr Mackay highlighted the impact that new technologies developed by Beef CRC have had on AACo’s business and profit
Deputy Prime Minister, Hon Mark Vaile MP at Beef 2006
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margins, as well as the overall impact Beef CRCs research is having on the global and local beef industries.
Awards
Over the 2005/2006 financial year, several CRC staff were recognised through prestigious national and international awards, including:
• A prestigious international award for distinguished overseas scientists to Professor John Thompson (July 2005) on behalf of the Korean government, to acknowledge John’s outstanding contributions to the advancement of agricultural research and development in Korea.
• Professor Dave Pethick from Murdoch University was awarded the Beef Improvement Association of Australia’s Howard M Yelland Award, their highest award, for services to the Australian Beef Industry (August 2005)
• Dr Toni Reverter from CSIRO, Brisbane was awarded the NSW Ministry for Science and Medical Research Eureka Prize for Bioinformatics Research (August 2005)
• Professor Bernie Bindon from the Beef CRC was awarded the 2005 Rabobank Red Meat Innovation Awards, Rural Press Beef Achiever of the Year Award (August 2005)
• Fellowships of the Association for the Advancement of Animal Breeding and Genetics (AAABG) were awarded to Professors Bernie Bindon, Mike Goddard and Hans Graser (September 2005)
• Professor Bernie Bindon received an honorary Doctorate of Rural Science awarded by the University of New England, recognising his extraordinary achievements through the Beef CRC and as a CSIRO livestock researcher (October 2005).
Changes to the Beef CRC Board
Shortly after the formation of the new CRC Board, CRC staff were very saddened by the sudden and unexpected death of Dr John Vercoe, a foundation Director of the CRCIII Board. John had been recently appointed as one of the 7 skills-based
L-R: Toni Reverter, Dave Pethick, Bernie Bindon
Directors of the new CRC Board and had already shown that his was the voice of sound commonsense, industry relevance, effective collaboration and above all, identification of solutions. John was always an unstinting supporter and wise advisor to CRC scientists, extension staff and managers. The CRC is now exploring options to establish a memorial to recognise John’s outstanding efforts on behalf of the Beef CRC.
The CRCII Board, very capably led by Mr Peter Frawley, deserve our most sincere thanks and gratitude for their efforts over many years in successfully steering the CRC through a minefield of research and semi-political difficulties, compounded by droughts and high grain prices that impacted on the CRC’s ability to undertake experimental cattle activities, to deliver outcomes of significant benefit to the Australian beef industry as well as a successful renewal process.
We also owe Professor Bernie Bindon a huge vote of thanks for his efforts in establishing and leading the first and second phases of the Beef CRC and for so capably leading development of the third phase.
Beef CRC Board: L-R Heather Burrow, Rob Backus, Grant Sutherland, Guy Fitzhardinge, David Siddle, Greg Robbins, Lucinda Corrigan, Keith Steele, Jay Hetzel
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Governance, Structure & Management
> Participants
> The Governing Board
> Board Sub-Committees
> Industry Sponsors
> Management Committee
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The CRC for Beef Genetic Technologies is incorporated as Beef CRC Limited a company limited by guarantee.
Participants
The Core Participants in the Centre are Meat and Livestock Australia, Meat & Wool New Zealand, NSW Department of Primary Industries, Queensland Department of Primary Industries & Fisheries, South Australian Research and Development Institute, University of Adelaide, University of New England, University of Queensland and Victorian Department of Primary Industries. There were no changes to the participants in 2005/2006.
The Supporting Participants in the Centre are CSIRO, Murdoch University, Northern Pastoral Group, Genetic Solutions, National Livestock Research Institute (Korea), Australian Lot Feeders Association, Genus, The Ohio State University (USA), Cattle Council of Australia and WA Department of Agriculture and Food.
Supporting participant agreements have been finalised with Murdoch University, The Ohio State University and the Department of Agriculture and Food, Western Australia.
These participants give the Centre a national, as well as an international focus. The partnerships which include R&D providers, as well as industry organisations enhance the CRC’s
ability to deliver outcomes to a wide range of end-users across Australia. In each state the outcomes are delivered by Participants with expert local knowledge and industry linkages.
The Governing Board
The role of the Board is to govern the Company. In governing the Company, the Directors act in the best interests of the Company as a whole. Senior management manages the Company in accordance with the direction and delegations of the Board and the responsibility of the Board to oversee the activities of management in carrying out these delegated duties.
In carrying out its governance role, the main task of the Board is to drive the performance of the Company to achieve its research outcomes. The Board also ensures the Company complies with its contractual, statutory and other legal obligations, including the requirements of regulatory bodies. The Board has the final responsibility for the successful operations of the CRC.
The Board meets at least 5 times a year as an entire Board. In addition the Board Committees meet several times a year as outlined in the Corporate Governance report in the financial section.
The Board comprises an independent beef industry Chairman, the CEO and 7 non-executive Directors appointed on the
basis of the skills they can contribute to the Board. Board members, including the Chairman and CEO, are directly elected by the Participants. The planned mix of skills on the Board is such that at least 2 Directors are highly experienced in R&D management, at least 2 Directors are highly experienced in beef industry issues and the remainder of Directors have specialist skills required by the Company (e.g. financial, legal, commercialisation etc). Currently, five of the nine Board members are independent of the Participants. Six Board members are from the private sector.
Governance, Structure & Management
BOARD MEMBER EXPERTISEMr Guy Fitzhardinge(Independent, Non-executive,Chairman)
Commercial cattle producer from NSW, past member of the Boards of Meat ResearchCorporation and Meat and Livestock Australia. Has postgraduate training in extensionand agricultural economics and committed to R&D and commercialisation of results.
Mr Rob Backus (Independent, Non-executiveDirector)
Northern beef industry and feedlot expertise and knowledge of the industry relevanceof genomics. Has had a close personal involvement in the Beef CRC since 1992, as amember of the Beef CRC Advisory Committee and a member of the third term RenewalCommittee.
Mrs Lucinda Corrigan(Independent, Non-executiveDirector)
Southern beef industry expert and beef seedstock business operator, with industrycommunication skills. Also a Director of the CRC for Plant Based Management ofDryland Salinity
Dr Jay Hetzel(Non-executive Director)
Genetics and genomics research and commercialisation background. Expertise in R&Dand Intellectual Property (IP) management and commercialisation, with knowledge ofCRCs.
Professor David Siddle(Non-executive Director)
Pro-Vice Chancellor (Research) at University of Queensland. Highly experienced R&Dmanager with extensive knowledge of CRCs and corporate governance and financial skills from diverse Boards and budgetary responsibilities through the University
Dr Keith Steele(Independent, Non-executiveDirector)
Business advisor with beef R&D management experience, genomics knowledge andcorporate governance and finance skills. IP commercialisation experience in Australiaand New Zealand. Current and former Director of 16 technology companies
Professor Grant Sutherland AC(Independent, Non-executiveDirector)
Acknowledged genetics expert, with experience of CRC management andcommercialisation of Intellectual Property resulting from Australian R&D. Co-founderof Bionomics Ltd and an Executive Director of Biolipids Pty Ltd and of New World BioLtd.
Dr Greg Robbins(Non-executive Director)
.yrtsudnIfeeBnrehtroNehtfoegdelwonktsilaicepshtiw,tsitneicserutsapdnalaminA16 years management experience within the Qld Department of Primary Industries andFisheries. Currently, General Manager of Animal Science for the QDPI & F.
Dr Heather Burrow(Chief Executive Officer)
Quantitative genetics R&D experience, specializing in genetic improvement of tropicallyadapted beef cattle. Twelve years management experience in the Beef CRC with 5years as Deputy CEO. Committed to delivery of results to industry
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Board Sub-Committees
Finance and Audit Committee
The Finance and Audit Committee is responsible for reviewing the integrity of the Company’s financial reporting and overseeing the independence of the external auditors. The current members of the Committee are Professor DAT Siddle (Chair) , Mr HG Fitzhardinge and Dr KW Steele. The Company Business Manager and CEO are ex-officio members of the Committee. The Audit Committee held two meetings throughout the year.
Intellectual Property and Commercialisation Committee
The Intellectual Property and Commercialisation Committee (IP&C) is responsible for providing guidance on IP management and commercialisation. The current members of the IP&C Committee are Professor GR Sutherland (Chair), Dr KW Steele and Dr GB Robbins. The Company’s Business Manager is an ex-officio member of the Committee The IP&C Committee held eight meetings throughout the year
Industry Impact and Adoption Committee
The Industry Impact and Adoption Committee (II&A) is responsible for providing guidance on strategies for industry uptake and adoption of CRC research. The current members of the Committee are Mr RWK Backus (Chair), Mrs LLF Corrigan and Dr DJS Hetzel. The Deputy CEO is an ex-officio member of the Committee. The II&A Committee held two meetings during the year.
Remuneration Committee
The Remuneration Committee assists the Board in fulfilling its responsibilities in respect of establishing appropriate remuneration levels and incentive policies for Directors and
employees. Dr KW Steele (Chair), Mrs LLF Corrigan and Professor GR Sutherland are the current members of the Committee, The Remuneration Committee held three meetings during the year.
Industry Sponsors
Generous sponsorship has come from commercial firms and organisations from across the beef business sector, including:• Australian Agricultural Co Limited• Australian Country Choice/Coles Supermarkets• Consolidated Pastoral Co• Northern Australian Pastoral Company• Ridley Corporation Limited• Stanbroke Pastoral Co• CSL Limited • Intervet Pty Ltd• AgReserves Australia Limited• Colonial Agricultural Company• Consolidated Pastoral Company• GRM International• International Animal Health Pty Ltd• Agricultural & Business Research Institute• Alcoa Farmlands• Elanco Animal Health• PrimeGro Limited• S Kidman & Co• Twynam Pastoral Company• Australian Lot Feeders Association• C&R Briggs• EA &G Maynard• GE & J McCamley• MDH Pastoral Company• J & SM Halberstater• Angus Society of Australia• Australian Poll Hereford Society
• Australian Association of Cattle Veterinarians• Australian Belmont Red Association• Australian Brahman Breeders Association• Australian Hereford Society• Australian Shorthorn Society• Beef Improvement Association of Australia
Management Committee
The day-to-day management of the Centre is the responsibility of the Management Committee comprising the CEO, Deputy CEO, Business Development and Commercialisation Manager and the Program Managers. The Committee meets at least 12 times a year by telephone conference or physical site meetings.
Board Sub-Committees
BOARD
ChairmanGuy Fitzhardinge
CEOHeather Burrow
D/CEOPaul Arthur
Finance & Audit Committee
ChairmanDavid Siddle
IP & Commercialisation
Committee
ChairmanGrant Sutherland
Industry Impact & Adoption
Committee
ChairmanRob Backus
Remuneration Committee
ChairmanKeith Steele
Industry & Scientific Reviews
Centre Forum
ChairmanGeoff File
P1High Quality Beef
ManagerDave Pethick
P2Feed Efficiency &
Responsible Resource Use
ManagerWayne Pitchford
P3Adaptation & Cattle Welfare
ManagerJohn Gibson
P4Female
Reproduction
ManagerJim Walkley
P5Education &
Training
ManagerJohn Thompson
Underpinning Sciences
ManagerMike Goddard
Business Development &
Commercial-isation
ManagerGeoff Allen
Secretariat
ManagerHeather Burrow
Management Committee
CRC Management Structure
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Context & Major Developments
> Industry Context
> Major Developments & Initiatives
> Commercialisation / Utilisation Strategies
> IP Management
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Commercialisation / Technology Transfer / Utilisation
> Commercialisation / Utilisation Strategies
> IP Management
> End-User Involvement
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Industry Context
The beef industry is at a pivotal stage in its history: with only 2.5% of the world’s cattle numbers, but 23% of the world’s beef trade, Australia can only retain leadership by producing to exacting specifications to satisfy consumers in extremely diverse markets, against fierce competition from northern and southern America.
The CRC aims to improve capacity to deliver high quality beef to Australia’s 110 global markets using cattle of known genetic merit for exacting specifications without compromising animal welfare or the environment. This will be achieved by selecting cattle for specific markets based on the genes they carry, not through artificial modification of their genomes. New technologies derived from our understanding of gene networks will then be used to enhance cattle performance.
Use of CRC technologies to increase market share for Australian beef producers is endorsed by an industry economic model known as The Livestock Revolution, which derives from “Livestock to 2020 – the Next Food Revolution” (Delgado et al., 1999; 2002) and is based on the International Food Policy Research Institute’s (IFPRI’s) global food model that uses data from 37 countries and country groups and 18 commodities. The model’s baseline scenario predicts that consumption of meat in developing countries will grow by 2.8% per year between the early 1990s and 2020. The corresponding developed-world growth rates are 0.6% per year. By 2020, developing countries will consume 100 million metric tons more meat, dwarfing developed-country increases of 18 million metric tons. Australia is best placed to supply the expanded beef component of the Asian markets.
In 2003, cases of Bovine Spongiform Encephalopathy (BSE) were reported in Canada and the USA and this resulted in a ban on beef imports from these countries by most of our north Asian trading partners. A similar ban was imposed in relation to Foot and Mouth Disease (FMD) outbreaks in Argentina, Brazil and Uruguay. These north and south American countries are our major competitors in the global beef trade, hence the change in the international marketplace due to the BSE and FMD cases means that Australian beef is in greater demand in north Asia, where quality beef is essential. This makes the need to achieve the Beef CRC’s outcomes even more imperative.
The Beef CRC’s mission is to capture the benefits of the international human and bovine genome projects and the ‘Livestock Revolution’ to improve the profitability, productivity, animal welfare and responsible resource use of Australian and global beef businesses through world-class gene discovery and gene expression research and accelerated adoption of beef industry technologies.
Major Developments and Initiatives
Establishing Beef CRC Ltd
The CRC for Beef Genetic Technologies was initially incorporated in June 2005, as a company limited by guarantee (Beef CRC Ltd). The members of the company are the nine core participants. The company’s operations are under the control of a largely independent governing board.
Official launch of the CRC
The CRC for Beef Genetic Technologies was officially launched on 13th December 2006 at the University of New England by Mr High Morgan AC, immediate past president of the Business Council of Australia, former Chief Executive of Western Minning and a Hereford breeder from Victoria.
Staffing beef CRC’s headquarters
While the CEO-designate was known in early 2005, Heather Burrow formally took up this role on 1 July 2005. Significant staff appointments during this reporting period included Geoff Allen as of Business Development and Finance Manager; Paul Arthur as Deputy CEO and Warwick Fraser as Communications Manager.
Purchases of Major Equipment
Two real-time Ultrasound Scanning machines were purchased as key equipment in reproduction research for ovarian and fat scans. A Tissue Lyser/Centrifuge was also acquired as key equipment for laboratory genomic procedures. Other equipment purchased included a farm utility vehicle, second hand tractor, and a feed mixer for the Tullimba Cattle Research Feedlot which supports the research programs.
Marker-assisted EBV model for BREEDPLAN
Work is underway to genotype all CRC I and CRC II animals for the seven commercially available GENESTAR DNA tests to provide data to deliver a marker assisted EBV model for BREEDPLAN developed by AGBU.
Unique Bos indicus SNPs
The international bovine gene sequencing project, coordinated in the United States, originally only looked at Bos taurus cattle. However, more than half of the Australian cattle herd is derived from Bos indicus breeds from tropical areas. It was therefore essential that genomic tools be developed for use specifically in tropically adapted cattle.
Context & Major DevelopmentsCommercialisation / Technology Transfer / Utilisation
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Beef CRC has collaborated with EMBRAPA in Brazil and the International Livestock Research Institute (ILRI) in Kenya to specifically develop a new genotyping tool for use in Bos indicus cattle such as the Brahman, Droughtmaster and Santa Gertrudis breeds. 7,000 new SNPs (single nucleotide polymorphisms) unique to Bos indicus have been identified and will now be used to assist in the discovery of genes found specifically in tropically adapted cattle.
Whole Genome Scans
As a result of the international bovine gene sequencing project, a 10K SNP chip, covering the bovine genome is now commercially available. The use of such chips to aid in the search for gene markers for economically important traits is commonly referred to as a whole genome scan. Two whole genome scans covering 792 animals were conducted by the CRC in 2005/2006 to aid in the search for gene markers for meat quality and age at puberty.
Commercialisation / Utilisation Strategies and Activities
Strategy
The commercialisation strategy to be used (see flow chart diagram) by the CRC for Beef Genetic Technologies (CRC III) recognises different types of products and processes arising from research and identifies appropriate pathways for their commercialisation (including IP and patent / trade secret protection where appropriate) and utilisation to achieve high value outcomes for industry. The strategy is made up of three interrelated components, as follows:
1. IP identification, protection and management.
This component is covered separately under the IP Management section
2. Commercialisation of IP
Expressions of interest were sought from organisations with expertise to help Beef CRC commercialise any IP that
arises from CRC research in future. The tick vaccine project was used as a model to develop the CRC’s commercialisation processes (see commercialisation flow chart diagram), so that by the time CRCIII has IP ready to commercialise, the processes will be established and the expertise required to complete the task will be available to the CRC. A preliminary feasibility assessment has been completed for the proposed tick vaccine. At this stage no new or improved products have been developed by CRC III and no IP commercialisation arrangements with industry have been entered into.
3. Communication, Awareness and Adoption
There was significant activity on this component of the commercialisation strategy. Distillation of research outputs into intelligent business solutions, continued. The highlight being the reprint of the book, “Producing Quality Beef ~ Opportunities for Beef Producers from the CRC for Cattle and Beef Quality”. Development and delivery of integrated training packages for both temperate and sub-tropical Australia also continued, and several training workshops and courses were delivered. Several talks were presented at major industry field days and events. Details on these activities are provided under Project 4.4 in the CRC II section.
The electronic online Livestock Library, is a collaborative project with Sheep CRC, with “free to air access”. It was
Livestock Library homepage
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publicly launched at in September 2005 and saw the number of registered users jump from 251 to 1,313 in six months.
To facilitate the accelerated adoption of CRC technology in Australian and New Zealand beef industry, Beef Profit Partnership teams were established. The teams are using the principles of accelerated adoption as part of a cycle involving measurement, monitoring and evaluation. The BPP groups are being documented as part of of the CRC III monitoring program that will underpin the achievement of CRC commercialisation outputs and profitability outcomes. Fifty Beef Profit Partnership teams have been initiated or are planned across Australia and New Zealand. They include supply chain groups (with Program 1) and regional producer groups. The breakdown of the teams across regions are:
• QLD 18 producer BPPs, 2 supply chain partnerships
• NSW 12 producer BPPs, 2 supply chain partnerships
• Vic 6 producer BPPs
• SA 3 producer BPPs
• WA 3 producer BPPs, 1 supply chain partnership
• New Zealand 3 producer BPPs
Details on the Livestock Library and the BPP groups are provided under Project 5.2.1 and Project 5.2.2 in the CRC III section.
All commercialisation milestones have been met, except milestone 2.1.3.1 which has been moved to June 2008 to allow for proof of concept studies to be completed.
IP ManagementIn readiness for IP commercialisation activities within CRCIII, the Board’s IP&C Committee developed an IP management and commercialisation policy in accordance with the National Principles of IP Management for Publicly Funded Research.
PatentsNo patents have yet been filed on behalf of CRCIII. However, the following patents were lodged on behalf of the CRCII owners and partners:
• Provisional Patent Application 2005906058 “Markers for tick resistance I” filed in name of CRCII Core Partners and DairyAustralia on 2 November 2005 (Inventor – Bill Barendse)
• Provisional Patent Application 2005906059 “Markers for tick resistance II” filed in name of CRCII Core Partners and DairyAustralia on 2 November 2005 (Inventor – Bill Barendse)
• Provisional Patent Application 2005906118 “Markers for dairy production traits I” filed in name of CRCII Core Partners and Dairy Australia on 4 November 2005 (Inventor – Bill Barendse)
• Provisional Patent Application 2005906117 “Markers for dairy production traits II” filed in name of CRCII Core Partners and Dairy Australia on 4 November 2005 (Inventor – Bill Barendse)
• Provisional Patent Application “QTL for improved feed efficiency, measured as net feed intake, in bovine animals”, covering 4 regions of the genome affecting NFI (Inventors – Wayne Pitchford and Cynthia Bottema) Filing date 7 December 2005.
• USA Provisional Patent Application “SNPs for improved feed conversion efficiency” (Inventors - Ben Hayes, Michael Goddard, Iona McLeod, Amanda Chamberlain) Filing date 5 Dec 2005.
Members of the South Australian Beef Profit Partnership
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CRC for Cattle & Beef Quality (CRCII)
> Summary of Results
> Program Updates
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The CRC for Cattle and Beef Quality delivered an excellent track record for achieving industry outcomes. The outcomes are many and include:
• Generation of the scientific explanation for the influence of marbling on beef eating quality, and production of definitive results to show the effects of hormonal growth promotants on beef eating quality.
• Production of world-first EBVs of feed efficiency (net feed intake) underpinned by CRC’s genetic parameters and the opportunity for indirect selection using Insulin-like Growth Factor-I (IGF-I).
• Generation of genetic relationships that highlight the antagonisms between retail beef yield, intramuscular fat, feed efficiency, tropical adaptation and female reproductive attributes.
• Discovery and patenting of 5 gene marker tests for marbling and tenderness, and licensing Genetic Solutions Pty Ltd to deliver the tests to the beef industry. Six provisional patents were filed in 2005/2006 as shown in the IP Management section.
• The undergraduate, postgraduate and industry training programs have had a major effect on skills of the meat industry workforce. These include 23 PhD and Masters students and thousands of undergraduates, TAFE students and industry practitioners. The graduate employment destinations of the 2005/06 postgraduate students are presented in the Education and Training section of this report.
Summary of results from three case studies on economic impact of three CRC II outcomes
• Meat Standards Australia (MSA) – Grading Scheme: The MSA economic analysis estimated that the cumulative retail value of the MSA system to 2004/05 is $159m (in terms of 2005 prices), with a projected benefit of $85m for the 2005/06 year.
• Net Feed Intake – Environmental benefit: The NFI economic analysis showed that NFI is a technology that allows profitability and environmental outcomes to be jointly achieved. Adopting the NFI trait has the potential to reduce enteric methane output in the range of 11% to 20% per animal after 25 years. Simulations accounting for differences between northern and southern production systems indicate that over 25 years a cumulative total of 568 Gg of methane would be abated. A minimum value for the saved methane output due to the adoption of RFI genetics in the national beef herd is estimated to be $125.3 million.
• Beef Profit Partnership – South Africa: The South African economic analysis estimated that the ACIAR-funded BPP
project increased revenue to the emerging farmers involved in the teams by >Rand 1.25 million over the period 2001-2005. The average was Rand 14,358 per farmer team per year.
Project 1.1 / 1.2 ~ Regulation of growth, carcase composition and beef quality
Mission
To develop a quantitative understanding of effects of nutritional regulation of growth at specific phases of an animal’s life on subsequent growth and development of carcase tissues, and of factors governing muscle metabolism and structure that impact on eating quality of beef.
Goals
• Quantify nutritional, genotypic and other regulators of cellular development and metabolism of carcase tissues
• Define key growth periods for nutritional regulation of desirable carcase attributes
• Quantify the influence of post-mortem conditions on specificity and activity of myofibrillar and cytoskeletal substrates of known proteolytic systems.
• Evaluate different production factors that influence muscle membrane composition and functionality and determine their impact on post-mortem muscle structure and biochemistry
• Integrate the outcomes from the above objectives into systems for improving eating quality
• Establish feeding and management strategies to more reliably meet premium beef specifications
Strategies and Progress
Communication, Education and Technology Transfer
Our emphasis in 2005/6 was on dissemination of the findings of our research to the scientific community and industry within our Communication, Education and Technology Transfer strategy. All experimental strategies are now complete, and information continues to be developed and published for scientific and industry dissemination.
The major outcome from the project during 2005/6 was to develop coherent, integrated information for the use of industry on effects of growth path on subsequent growth, carcass and yield characteristics, and on beef eating quality. This information was drawn from scientific studies in Beef
CRC for Cattle & Beef Quality (CRCII)
Sub Program �. Strategic Science to Deliver Beef Quality
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CRC1, and from the major growth path studies on effects of growth during the prenatal, pre-weaning and immediate post-weaning periods conducted within Beef CRC2. Initial scientific publications from the Beef CRC2 studies which provide the most commercially relevant results. They have been published in a CRC Special Edition of the Australian Journal of Experimental Agriculture. Scientific papers on more specific aspects of cow-calf management, growth and carcass composition, metabolism, muscle cellularity and structure, and molecular biology are in various stages of preparation and will continue to be submitted for publication in international scientific journals during the next few years. Aspects of this research will also provide a platform for Strategy 1.1.3 (Proof of Concept/Gene Expression) within the new CRC for Beef Genetic Technologies.
Our formal commitment to the Milestones within Project 1.1/1.2 will be met with the completion of economic modelling of growth path effects in the Beef-N-Omics program, and with the conduct of a workshop on how best to package and extend the results of research on growth paths, to identify any outstanding needs to ensure the information in decision making by industry. The workshop is being coordinated within Strategy 4.4.
The reader is also referred to previous CRC Annual Reports for details of major outcomes of the other strategies within the program, namely:
• Protein turnover in vivo
• Protein degradation – cell culture and proteomics
• Membrane functionality and post-mortem biochemistry
• Quantitative methods in vivo
• Methods to alter growth in utero and pre-weaning
• Extreme post-weaning nutrition in tropically adapted cattle
• Extreme genotypic and early-life nutritional influences
Project 1.3 ~ Regulation of intramuscular fat in beef cattle
Mission
To establish a mechanistic and functional understanding of the factors that determine the extent and pattern of fat development within bovine skeletal muscle, and to make this available to the beef industry so that they may improve the consistency with which their cattle meet marbling specifications.
Objectives
• To define the regulatory steps in the development of adipocytes in bovine muscle using molecular, cellular and physiological techniques, and hence to develop a mechanistic understanding of how background genetic and
environmental variation impacts on adipocyte number and size;
• To define the key nutritional factors that influence intramuscular fat deposition and development and hence, define the nature of genetic influences on these;
• To utilise the above knowledge, in conjunction with methodologies such as candidate genes, video image analysis, real-time ultrasound and novel nutritional technologies to specifically target intramuscular fat specifications in Australian beef production systems.
Strategies and progress
Research intensity significantly reduced in project 1.3 in the 05/06 term consistent with the planned budget expenditure. Nonetheless scientists from 5 organisations remained engaged at some level, particularly as novel approaches to some of the unresolved issues from project 1.3 were incorporated into the plans for the CRC for Beef Genetic Technologies. Collaboration between staff within projects 1.1/1.2, 1.3 and 1.4 continued during the year, showing again that operational boundaries between projects lose relevance as science progresses.
We focussed our work in this period on finalising data collection, completing analyses, drafting manuscripts and presenting outcomes to key stakeholders. A small amount of experimental development continued on the prototype visual methods for quantification and characterisation of marbling distribution.
Definition of developmental milestones for marbling in cattle
Data from the Grafton growth path studies were analysed and there were no significant effects on the extent of marbling deposition other than the genetic and sex effects that are well known. These findings are the result of long-term investments made through projects 1.1/1.2 and 1.3. Another series of papers related to gene expression changes resulted from collaborative work funded through project 1.4. The final conclusions of this body of work as it relates to marbling were presented at the “Beef – The Leader” conference. In general, project 1.3 has confirmed the role of Wagyu genetics, gender and developmental age in the expression of marbling, but we have not developed reliable practices for increasing marbling. Our current understanding of marbling has been communicated to interested producers through training and extension packages. There is still a need for studies into early-life growth path effects on variation in marbling within genotype groups.
The vitamin A-depletion studies were accepted for publication in the journal “Lipids”. Whilst these vitamin A treatments were associated with significant increases in the expression of intramuscular fat in Angus cattle, the technique was not endorsed
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for extension to industry because of the many risks associated with purposeful undernutrition of production animals.
Project 1.3 has had most impact on the feedlot sector, where we have contributed to increased use of high ME diets, endorsed the use of Wagyu F1 and purebred cattle in feedlots, and refuted some unfounded perceptions that existed in industry at the time of instigation of the project (e.g. beer massage for high marbling; longer feeding = higher marbling).
The project has also worked on a package of intellectual property relating to measurement of the distribution of marbling in beef, and sought commercial co-investment in the further development of that technology. This IP has been licenced into CRC III. It is likely the IP will be released into the public domain via publication, so it can be used more generally by the processing industry.
The project continued to work on aspects of marbling distribution in Angus and Hanwoo cattle from Korea. “Predicting beef marbling: innovative method using 3D image analysis” was a project sponsored by the Australia-Korea Foundation and Beef CRC which aimed to explore the correlation between ultrasound scanning and three-dimensional structure of marbling, and identify parameters affecting ultrasound scans for marbling. The work involved Angus steers in Australia and Hanwoo steers and bulls in Korea. The Australian steers were part of the vitamin A-depletion experiment. There were no differences between the ranges of IMF% in the rib-eye region in the breeds or between the countries. However, vitamin A depletion promoted higher IMF% in Angus steers, as it did in Hanwoo steers.
The distribution of marbling flecks differed between the breeds and levels of vitamin A fed. Reduced levels of vitamin A produced more regular flecks in Australian Angus steers. Hanwoo cattle produced more flecks which were smaller and presumably more desirable from the consumers’ perspective. The eccentricity of marbling flecks differed between the breeds, but vitamin A depletion
in Angus cattle produced more rounded flecks, similar in shape to the marbling flecks in Hanwoo steers.
The moderate, positive correlations between ultrasound scanning and various marbling fleck parameters such as number, area, minor axis (width) and ellipticity (irregularity) demonstrated the distributional properties of marbling have an impact on scanning results. Both breed and vitamin nutrition are important factors affecting marbling parameters. Hanwoo and Angus cattle differed in marbling and marbling fleck characteristics. Moreover, dietary Vitamin A affected marbling characteristics. To measure IMF% and marbling accurately using ultrasound,
marbling fleck parameters may need to be considered.
The project also developed a new technique to visualise marbling in three dimensions and quantify distributional parameters. Two main algorithms were developed to: (1) distinguish fat from muscle based on high-resolution pictures taken from frozen slices and estimate the number of marbling flecks and the fleck area, and (2) develop and describe various marbling fleck parameters such as eccentricity, orientation, length and width, branching and position.
Project 1.3 completed its training activities in the 05/06 period. One undergraduate student (Louise Hale from UQ) completed her Agriculture 4th year project using Beef CRC Grafton samples and completed a thesis with distinction. One postgraduate student (Peter Allingham) completed his MSc thesis and successfully upgraded to a PhD program at Monash University. The final research chapter of the PhD will not require further resources from the CRC. However the thesis will continue to attribute two research chapters to the support of Beef CRC II when completed. An AgSci Honours student was also trained at University of Adelaide.
Project 1.4 ~ Functional Genomics of Beef Quality
Mission
To characterise genetic, biochemical and environmental interactions that contribute to beef quality. To use this knowledge to develop gene markers and to contribute to the development
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Experiment Chips Conditions Valid Signals
1. Grafton Diets 7 4 189,3152. Rockhampton 14 3 353,8403. Rocky Time Course 24 6 791,0704. Japanese Black 18 6 451,3545. Adipogenesis 15 4 410,9126. Grafton Foetal 25 8 838,3887. Grafton Breed × Time 21 6 712,6538. Adelaide Vitamin A 12 6 278,3859. Adelaide Jersey-Limo 11 4 263,732
Total = 147 47 4,289,649
Table 1. Summary of Beef CRC expression data performed using the Beef CRC bovine muscle and fat cDNA microarray chip
Marbling in beef
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of treatments and management strategies for the consistent and sustainable supply of high quality beef products.
Goals
• Establish microarray reagents using cattle muscle and adipose and foetal tissue cDNA libraries and inputs from the CRC gene mapping activities, adipogenesis and myogenesis models and other cattle EST resources
• Characterise expression of cattle muscle and adipose tissue genes during the course of different experimental treatments imposed on cattle in projects 1.1 / 1.2 and 1.3
• Characterise expression of candidate genes identified in Project 2.1
• Establish correlations between different beef quality outcomes, treatments, genotypes and changes in gene expression patterns
• Identify biochemical pathways and gene regulatory networks of key importance in the determination of beef quality outcomes
• Identify possible candidate genes for beef quality outcomes
• Use the information gained from these experiments to contribute to genetic, nutritional and other management strategies to manipulate beef quality outcomes.
Strategies and Progress
Project 1.4 used gene expression-based approaches to study genetic, biochemical and environmental interactions that contribute to beef quality. Towards this goal, the project has developed RNA based technologies (microarray and quantitative RT-PCR) for bovine muscle, with a focus on marbling development. The project team studied bovine muscle gene expression in a number of animal experiments and made inroads into the establishment of cell culture models for intramuscular fat development. Ultimately, the knowledge generated by gene expression technology will be used to develop gene markers and contribute to development of treatments and management strategies for the consistent and sustainable supply of high quality beef products.
The main goals for Year 7 were to:
1. Complete and document microarray experimentation and to publish the results in the international literature
2. Complete and document cell culture functional studies
3. Document network models for muscle gene regulation based on gene expression data
4. Develop a “proof of concept” for an early marbling phenotype biomarker
Complete and publish microarray experimemntation
The microarray experimentation conducted on the Japanese Black vs Holstein breed comparison identified a list of genes that were markedly elevated in the muscle of young (11 mo) steers of the Japanese Black breed. To investigate whether expression of these genes in the longissimus muscle (LM) at an early stage was correlated with marbling in later life, we profiled 4 individuals from a group of Wagyu x Hereford and Piedmontese x Hereford animals (project 1.1/2), from which serial biopsies (3, 7 and 12 months) and intramuscular fat (IMF) data were available. Three of the adipogenesis-related genes identified as significant in the initial study were found to be significantly more highly expressed in the Wagyu x Hereford animals examined here. The study indicates that relevant intramuscular fat cell development occurs relatively early in life (3-7 months of age).
Cell culture functional studies
A major goal of this work was to establish whether there is a role for thyroid hormone signalling in triggering or enhancing fat cell development in bovine muscle. Our hypotheses on thyroid hormone involvement in bovine intramuscular adipogenesis were based largely on the dramatic THRSP expression differences observed in bovine skeletal muscle with respect to marbling development.
When thyroid hormone was added to cultures of cells isolated from bovine SC fat, the thyroid hormone seems to inhibit the differentiation process induced by the classic adipogenic induction medium (based on insulin). In cells that were treated with induction medium + thyroid hormone, the expression levels for adipogenic indicator genes were very low compared to the levels in cells that were treated with induction medium or with thyroid hormone alone. This observation was confirmed by Oil Red O staining at 14 days post-treatment (Figure 1).
Network models arising from joint analysis of microarray results
Beef CRC expression data has been an invaluable resource to develop methodology in the area of reversed engineering of gene networks. Mixed-model equations were shown to provide a robust mathematical framework to (1) jointly analyse expression data resulting from seemingly independent experiments (experiments 2, 4 and 5 in Table 1; and (2) to adjust data prior to the computation of gene co-expression measurements (experiments 1 to 5 in Table 1. Based on these approaches, a preliminary gene interaction and regulatory network for bovine skeletal muscle has recently been proposed.
The entire data set has been jointly analysed to successfully generate a gene network with 822 genes. Our results not only recapitulate the known biology of muscle, but have revealed some of the subprograms of expression of the different structural components of skeletal muscle.
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Figure 1: Bovine cells isolated from SC fat under differentiation by induction medium or induction medium+ thyroid hormone. The cells were stained with oil red O stained at 14 days post-treatment. The red dye indicates the presence of triglycerides. Microphotographs were taken at 400X. A: control cells; B: induction medium treated cells; C: induction medium + thyroid hormone (500nM) treated cells.
Table 2: Results of “Factor A” antisera tests using mouse and bovine substrates
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Early Marbling Biomarker
One possible avenue for commercialisation of gene expression results is the development of biomarker assays for differentially expressed gene products that may be detectable in peripheral blood. We carried out a small study, using commercially available antibodies to mouse or human proteins, to test the hypothesis that gene expression differences for certain adipogenic genes may be mirrored and detectable in serum samples. Stored serum samples from the first 4 postnatal sampling time points of Wagyu x Hereford and Piedmontese x Hereford animals (project 1.1/2) were tested with polyclonal and monoclonal antisera against “Factor A”, which has consistently been shown to be differentially expressed early in the development of marbling muscle. Unfortunately, we were unable to detect material in the bovine serum that could cross-react with the antisera (Table 2). As we did not have a positive control, we are unable to determine whether the failure to detect was due to the absence of the molecule from the sera or because of a lack of cross-reactivity.
Development of tests based on bovine peripheral blood nevertheless presents an attractive option for gene expression-based commercialisation and warrants future investment in proteomics and antibody-based approaches.
Project 2.1 ~ Genetic markers for beef quality and production traits
Mission
To develop genetic marker technologies that enhance selection techniques and ensure the production efficiency, product quality and consistent supply of domestic and export cattle.
Goals
• Fine scale map genes for carcase and meat quality and tropical adaptation, based on genes mapped to broad chromosome regions in CRCI and elsewhere.
• Map to broad chromosome regions and then fine scale map genes for net feed efficiency.
• Test candidates for the genes in objectives 1 and 2 or develop
haplotypes of markers so these genes can be selected using DNA tests that are not specific to a single family.
• Develop single nucleotide polymorphisms (SNP) over chromosomal regions and genes identified in objectives 1-3. Develop DNA micro-arrays based on these SNP for economically typing cattle for these genes.
• Determine the effect on adaptability of genes discovered by their effect on carcase and meat quality and the effect on meat and carcase quality of genes for adaptation.
• Demonstrate the use of DNA based tests to select commercial cattle for carcase and meat quality and adaptability.
Strategies and Progress
This year this project has discovered 2 new markers for marbling, 1 for retail beef yield, 31 for tick resistance and 100 for feed conversion efficiency. These markers are being tested in additional cattle and those that are confirmed as useful for selecting cattle will be commercialised.
The traits targeted by this project are marbling, tenderness, retail beef yield, tick resistance and feed conversion efficiency. For each trait our aim is to map genes that affect the trait, identify DNA markers that can be used to select for the trait and commercialise these markers so that cattle breeders can use them. Already this process has resulted in the ‘GeneStar’ tests for tenderness and marbling. However, most economic traits are controlled by many genes as well as environmental effects, so we are seeking to discover more markers for marbling as well as the first markers for retail beef yield, tick resistance and feed conversion efficiency (FCE).
To do this we have established a ‘pipeline’ that commences with mapping the gene to a broad chromosome region, then fine mapping it to a small region, identifying candidate genes within that region and testing them to see if there are variants of the gene that affect the trait. If we find variants that affect the trait these form the basis for a commercial DNA test that can be offered to cattle breeders. Some traits such as marbling have completed the pipeline whereas other traits such as FCE are still progressing through it. In the last 12 months a new technology has emerged to short-cut this pipeline a little. A company in the USA offers a service to simultaneously type cattle for 10,000 markers. This allows us to combine the initial mapping and fine scale mapping of genes in one step. We have used this technology to speed up the search for markers for tick resistance and FCE.
Although the CRC leads the world in DNA markers for beef cattle, other researchers in other countries also discover markers that they claim could be used to select cattle. The CRC tests some of these markers to see if they would be useful in Australian cattle. This should help to make available to Australian cattle breeders the best suite of markers that are available.
Marbling
Genes affecting marbling had already been mapped to chromosomes 3, 5 and 14. Ninety-one single nucleotide polymorphisms (SNPs) were discovered on these chromosomes and used to fine map the genes for marbling. Markers in 2 genes were found to be significantly associated with marbling.
Published markers in the leptin, HMGA2 and stearoyl-CoA
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Figure 1. Number of cattle tested for NFI by industry to 2005
Sub Program �. Innovative Technologies for the Beef Supply Chain
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desaturase genes were found to have no significant effect on marbling (although leptin may affect sub-cutaneous fat depth), but a marker in the growth hormone gene is associated with marbling.
Retail beef yield
A gene affecting retail beef yield had already been mapped to a broad chromosome region. 10 SNPs in this region were discovered and typed on cattle from CRC I where beef yield was accurately measured. One SNP showed a significant association with retail beef yield, especially in Santa Gertrudis cattle. This association is now being confirmed in additional cattle.
Tick resistance
This project was carried out with funding from Dairy Australia and sought to find DNA markers useful in both dairy and beef cattle. More than 2400 dairy cows were bled, DNA extracted and the number of ticks they were carrying counted. A subset of these cattle were genotyped for 10,000 SNP markers by the new Whole Genome Scan technology. 31 of these markers had a significant (p<0.001) association with tick count. In 2 cases the SNPs are in the same chromosome regions that had been previously shown to contain genes for tick resistance in beef cattle.
Feed conversion efficiency
Using the lines of Angus cattle selected for high and low efficiency at Trangie Research Station, five chromosomes were mapped for genes affecting net feed intake. Seven regions containing genes for efficiency were found and 5 of these overlap with regions discovered in Jersey x Limousin cattle at University of Adelaide.
A subset of 380 Angus cattle were genotyped using the 10,000 SNP panel. 100 SNPs had a significant association with efficiency and some of these map to the chromosome region previously discovered in the Angus and Limousin x Jersey cattle.
The physiological pathways affecting efficiency have been investigated and pathways that are associated with efficiency have been found. This knowledge of physiology combined with the SNP markers should help us to identify the actual genes causing variation in efficiency. In the meantime we are verifying the significant SNPs in additional cattle. If this is successful we will commercialise the useful SNPs as DNA markers for feed conversion efficiency.
Project 2.2 ~ Improving the Efficiency of Feed Utilisation for Beef Production
Mission
To reduce the cost of beef production through genetic improvement in efficiency of feed utilisation.
Goals
• To utilise existing scientific information to develop the NFI technology for industry application
• To develop and implement educational and extension strategies to improve the adoption rate of NFI technology by
industry
• To evaluate key genetic relationships between NFI and other economically important traits
• To develop lower cost methods to identify animals that are superior for NFI
• To develop optimal breeding designs for use by industry.
Develop and extend net feed intake technology to industry
This strategy aims to foster the roll-out of net feed intake technology by providing support for seedstock breeders measuring net feed intake on their animals, and through a targeted extension campaign to improve awareness and show commercial beef producers how they can improve profitability by selection on this trait.
NFI test data for industry cattle continued to be submitted to NSW DPI at Trangie. Data collected during NFI tests are checked and processed, with summarised information sent to clients and to ABRI for loading on the NBRS database. The number of animals tested by industry was 163 in 2005 (Figure 1), bringing to 3,622 animals tested by industry to date. The number of cattle being tested appears to have plateaued. Factors contributing to this have previously included the restricted test facility capacity available for private testing, the strong spring/autumn calving in southern Australian herds and the impact of drought on money available to spend on private testing. The commercial release of the IGF-I bloodtest for NFI in 2003 provided a less expensive way to find genetically superior bulls.
This year the Project 2.2 team wrote or presented 9 scientific journal papers, 9 scientific conference papers and 13 other publications including field-day handouts, seminars, and a research review.
Ben Wood submitted his PhD thesis at UNE on the cost-effectiveness and outcomes from investing in NFI testing, IGF-I tests and gene-marker tests. Visual-basic models based on Ben’s work will be used to help answer cattle producer’s questions
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Figure 2. EBV for NFI for all Angus and Hereford cattle (accuracy >19%) and for sires (accuracy >49%). IGF-I data was first used for EBV published for Angus in 2004 and for Hereford in 2005.
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about the merits of including NFI in their breeding decisions.
Evaluation of key genetic relationships between NFI and other economically important traits for beef production
This strategy is aimed at filling the key gaps remaining in knowledge of genetic relationships between net feed intake and other economically important traits.
Genetic correlations between the seedstock and steer feedlot measures of feed efficiency were reported in the paper presented at the “Australian Beef-the Leader” Conference held in Armidale in March 2006.
Steers from the third (final) cohort of the progeny test at the Trangie Agricultural Research Centre were backgrounded at the Glen Innes Research Station. From these, 136 steers were chosen for NFI testing at the CRC “Tullimba” Research Feeedlot. This test concluded in April 2006 and their data have been processed and entered into the Angus NBRS database.
Evaluation of the IGF axis an indirect marker for feed efficiency
Project staff continued to co-ordinate the collection and dispatch of IGF-I bloodspot cards for CRC and industry cattle destined for NFI tests, and to check results before entering the data into AGBU and ABRI databases.
The Primegro insulin-like growth factor-I (IGF-I) bloodspot test to identify cattle genetically superior for feed efficiency was launched November 2003. The impact of the test was to rapidly increase the number of bulls with EBV for NFI in the Angus breed, doubling the number of animals with reportable NFI EBV in their January 2004 sire summary, and more than doubling that number again in 2005 (Figure 2). Hereford/Poll Hereford was the next breed in 2005 to use IGF-I data in calculating NFI EBV.
Angus and Hereford/Poll Hereford remain the only breeds to publish NFI EBV. Over the same period the number of new animals with NFI test data has declined (Figure 1). However, IGF-I data alone cannot produce an accuracy of 50% or better, this being the level required for a sire EBV to be published in Breedplan. Feed intake and NFI records on individual sires and/or relatives are still required if higher accuracy EBV are to be produced.
This software to achieve multi-trait models for Angus has been developed but in consultation with the major cattle breed societies, this has not yet been implemented in Group Breedplan.
NFI EBV continue to be computed using a univariate model. Including NFI and IGF-I data in the full Group Breedplan multi-trait model for Angus and Hereford will allow better prediction of the response to selection in breeding programs, and Breed-Object selection indexes to reflect information on genetic variation in feed efficiency. The breed societies are concerned about possible antagonistic associations between selection for low IGF-I (improved NFI) and cow fertility traits.
Project 2.3 ~ Links between the genetics of beef quality and components of herd profitability in northern Australia
Mission
To increase the knowledge of genetic relationships between components of herd profitability in northern Australian environments, to improve efficiency and product quality without unduly compromising breeder herd performance or adaptability.
Goals
• Determine the correlated responses to selection for retail beef yield percentage and intramuscular fat percentage on body composition, efficiency of feed utilisation, adaptability to stressors of tropical environments and female reproductive attributes and estimate the relationships between these traits in tropically adapted cattle.
• Demonstrate the use of genetic markers to select commercial cattle for carcase and meat quality and adaptability.
• Extend the Australian and South African beef genetic evaluation schemes for Belmont Red and Bonsmara breeds to estimate breeding values for traits of economic importance across both countries.
Strategies and Progress
This project targets the pivotal issue in Australia’s beef genetic improvement dilemma: Can we change carcase and beef quality attributes of beef cattle without unduly compromising key fitness traits like reproductive performance and adaptation to harsh environmental stressors? Industry outcomes from the project are targeting multiple traits and multi-faceted strategies including carcase and beef quality, feed efficiency, female fertility and adaptation to tropical environments using a range of tools such as Estimated Breeding Values (EBVs), DNA markers, ultrasound scanning and meat processing and cattle management strategies that will impact on most sectors of the Australian beef industry.
Except for the last measures of first-calf post-partum re-conception that were recorded at weaning in April-May 2006, data collection for the project was complete in 2005 and data
Figure 1. Groups of traits being targeted by this project (shown on diagonal) and genetic relationships (rg) between the groups of traits that will identify the direction and magnitude of the trade-offs that will occur as a result of selection for the trait shown on the diagonal. Phenotypic relationships (rp) can be inferred in the lower quadrant of the matrix.
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analyses, writing up the results for scientific and industry use and delivering the results to industry have been the focus of project activities over the past year. Figure 1 outlines a summary of the genetic analyses that have been undertaken or are now underway. Squares on the diagonal indicate groups of traits being targeted by the project, including:
• Steers: repeated measures of growth, net feed intake, ultrasound scans for carcase attributes and scores for a full range of structural and temperament traits
• Heifers: repeated measures of growth, ultrasound scans for carcase attributes and scores for a full range of structural and temperament traits
• Heifers: age, weight and fatness at puberty + repeated measures of ovarian activity between 200kg and time the heifer joined the breeding herd
• Steers and Heifers: repeated measures of resistance to ticks, worms, buffalo flies, heat stress and dry season nutrition (when the stressors were present)
• Steers: a full range of carcase and beef quality attributes including retail beef yield, intramuscular fat percentage and beef tenderness with one side of the carcase hung by the Achilles tendon and the other side Tenderstretched;
• Breeding females: repeated ultrasound scans for reproductive function + complete measures of joining, calving and re-breeding).
Each group of traits was analysed separately to estimate variances and heritabilities for every trait. Those analyses are largely complete and preliminary results published. Of greater interest to most beef producers though are the genetic (future herd and achieved by use of breeding strategies – shown in the upper quadrant of the matrix pictured in Figure 1) and phenotypic (current herd and achieved by management / non-genetic approaches - logically would fit into the lower quadrant
of the matrix in Figure 1) relationships between these groups of traits as well as the supplementary economic analyses. These additional analyses are now underway.
In addition, the project data are being used to either discover new DNA tests (e.g. for reproductive attributes in Program 4 of the new Beef CRC) or to validate potential DNA markers discovered in other cattle populations (e.g. for net feed intake in Program 2, where markers for NFI discovered in the Trangie Angus population are currently being validated in this population).
Delivery of these research outputs and industry outcomes over the next 12-18 months will be through CRCIII Program 4. The very wide scope of the traits measured in the project, the large number of repeated measures for many of the traits and the degree of accuracy of the measurements mean the project’s dataset will continue to have a very significant impact on the development of recommendations for northern Australian beef producers for many years to come.
Genetics of reproductive attributes in Brahman and Tropical Composite females
Female reproductive performance is an important component of profitable beef production and can be improved by genetic and non-genetic means. Several studies have shown large within- and between-breed differences in fertility for tropical cattle breeds. However, female fertility traits are expressed relatively late in life, are sex limited, are often difficult to measure and are generally lowly heritable, making genetic improvement difficult. To achieve higher rates of genetic progress requires measures that can be recorded earlier, that are heritable and that are correlated to the underlying profit trait. One trait that may influence maiden calving performance is age at puberty.
The genetics of heifer pubertal traits and their associations with female reproductive performance were estimated using records from 2,115 heifers representing 2 tropically adapted genotypes
Project 2.3 Brahmans at Toorak Research Station, Qld
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raised in northern Australia. Heifers were ultrasound scanned for ovarian activity every 4-6 weeks to determine age at first observed corpus luteum (CL). Heifer live weight (WTCL) and ultrasound scanned fat depth (FATCL) were also recorded at this time. Heifers were mated at ~2 years and genetic and phenotypic relationships were estimated between days to calving (DC1), calving success (CS1) and age at first CL (AGECL).
Summary statistics for pubertal traits are presented in Tables 1 and 2 for Brahmans (BRAH) and Tropical Composites (TCOMP) respectively. Mean AGECL was 750.6 and 650.8 days for BRAH and TCOMP. Both breeds showed considerable variation (18% CV). Differences in the raw means reflected breed, location, birth month and cohort effects.
BRAH and TCOMP were not significantly different for WTCL (337 and 331 kg, respectively) but BRAH were on average 84 days older for AGECL, 1.3 mm fatter and had significantly lower percentage PRIORCL, longer DC1 and lower CS1 compared to TCOMP (Table 3). The reduced percentage of BRAH heifers showing a CL prior to mating clearly influenced the reproductive performance for the first calving (DC1 and CS1). However it is not possible to extrapolate genotype differences outside the range of environments in the experiment. TCOMP were purposely not allocated to the Swans location because it was perceived they would be poorly adapted and reproductive performance would have been compromised.
Age at first CL was moderately to highly heritable: 0.57 and 0.52 for BRAH and TCOMP respectively. Other pubertal traits were also moderately heritable. Heritability estimates for DC1 and CS1, were 0.16 and 0.18 for BRAH and 0.11 and 0.08 for TCOMP respectively. DC1 and CS1 were genetically correlated with AGECL, particularly for Brahmans (0.87 and -0.58 respectively).
The ultrasound ovarian scanning technology and scanning protocols used in this project have delivered a very powerful means by which to estimate genetic differences in age at puberty and associated traits and genetic correlations with female reproductive performance traits. The study has shown significant differences between genotypes, locations and birth months on AGECL. These differences could be used to develop management strategies to improve AGECL. Selection to improve first parity female reproductive performance is feasible in both genotypes. For Brahmans, AGECL could be used as an indirect selection criterion provided it can be measured cost effectively in industry. Associations with lifetime reproductive performance will be required before final recommendations can be made on recording and selection breeding schemes.
Genetics of growth and feed efficiency in Brahman and Tropical Composite steers.
The project investigated links between carcase and feed efficiency traits and female reproductive fitness in northern Australia. Following weaning, steers were run in cohorts on cooperating properties and, following the growout phase, were feedlot finished for a mean of 112 days. Steers received
an oestradiol-based growth promotant during grow-out and finishing. Heifers were run in cohorts on 4 research stations across Queensland as described above.
Genetic correlations for steer feed intake and Net Feed Intake (NFI) with growth traits and fatness were estimated separately for Brahmans and Tropical Composites. Heritability of NFI was 0.24 and 0.38 for Brahmans and Tropical Composites respectively. Genetic correlations between NFI and growth, hip height and P8 fat depth at feedlot entry (rg = -0.68, -0.41, -0.56 respectively) indicated these traits could be exploited to indirectly improve NFI in Brahmans, but were of little use for the Tropical Composites. IGF-I, sampled at feedlot entry and feedlot exit, had a negative correlation with NFI for these cattle treated with hormonal growth promotant.
Genetics of carcase and beef quality in Brahman and Tropical Composite steers
Meat tenderness can be affected by cold shortening under conditions of rapid chilling relative to the rate of decline in muscle pH post-slaughter. Application of processing techniques such as electrical stimulation, tenderstretching and correct aging of meat can be used to overcome the effects of cold shortening, but it is not known whether beef tenderness measured with or without correct application of processing techniques to overcome cold shortening is actually measurement for different attributes (and therefore whether selection to improve tenderness based on measurements of carcases that have been processed using/not
Trait N Mean s.d. Min. Max.AGECL (days) 1007 750.6 142.1 394 1211WTCL (kg) 993 334.4 44.8 196 485FATCL (mm) 951 4.47 2.19 1.0 15.0PRIORCL (%) 1008 0.51 0.50 0 1DC1 1020 346.4 49.8 279 423CS1(%) 1020 0.71 0.45 0 1
Table 1. Trait means, standard deviations and ranges for Brahmans
Trait N Mean s.d. Min. Max.AGECL (days) 1108 650.8 119.5 344 945WTCL (kg) 1094 329.6 45.9 206 474FATCL (mm) 1083 2.90 1.66 0.5 11.0PRIORCL (%) 1108 0.79 0.41 0 1.0DC1 1115 318.9 39.0 275 425CS1(%) 1115 0.90 0.31 0 1
Table 2. Trait means, standard deviations and ranges for Tropical Composites
AGECL(days)
WTCL(kg)
FATCL(mm)
PRIORCL(%)
DC1(d)
CS1
GenotypeBRAH 757 337 4.6 46 348 0.69TCOMP_ST1 673 331 3.3 74 323 0.86overall sed (17) (6) (0.3) (5) (4) (0.04)
LocationBrian Pastures 652 334 2.9 79 322 0.90Toorak 691 322 3.9 79 335 0.76Belmont 711 354 4.3 61 328 0.84Swans Lagoon 804 323 4.5 42 356 0.62overall sed (12) (4) (0.2) (4) (3) (0.03)
Birth month2
September 618 329 3.5 91 322 0.88November 703 336 3.7 71 324 0.88January 773 335 4.7 34 345 0.74March 854 341 4.6 9 392 0.28overall sed (20) (8) (0.4) (7) (7) (0.06)1 TCOMP_ST = sub-set of TCOMP representing only stabilised genotypes2 number of months reduced for ease of reporting
Table 3. Least squares means for heifer pubertal and calving traits
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using best practice will be effective). It is possible that alternative methods of hanging of carcases such as tenderstretch may reduce the amount of variation in shear force values. Hence, one aspect of CRCII Project 2.3 was to examine genetic parameters in carcases from steers where one side of the carcase was hung by the achilles tendon and the other was tenderstretched.
Preliminary estimates of heritabilities pooled across Brahmans and Tropical Composites show that all traits except MSA pH showed significant amounts of genetic variation and large differences between sires for their progeny performance. Research is currently underway to estimate the genetic (and phenotypic) correlations between the live steer traits and most importantly with their half-sib heifer reproductive performance traits.
Additional preliminary results shown in Table 2 clearly indicate significant benefits accrue from use of Tenderstretch. The benefits of tenderstretch were larger in poorer quality carcases and had the greatest effect on shear force (tenderness), with the greatest favourable effects seen in the toughest carcases. Brahmans and Tropical Composites benefited equally from the use of tenderstretch. Large sire differences for tenderness existed, but these differences were significantly reduced for shear force in carcases that had been tenderstretched.
Correlations between shear force measures in achilles-hung vs. tenderstretched carcases in Brahman, Tropical Composite and combined breed steers show the genetic correlations are significantly higher than the phenotypic correlations, indicating the relationships are strongest at the genetic level. They also indicate that selection to improve tenderness using measures of tenderness based on either achilles-hung or tenderstretched carcases will be equally effective, with only minor re-ranking of sires if the processing methods were to be altered.
Project 2.4 ~ Managing Stress to Improve Cattle Welfare and Beef Quality
Mission
To enhance cattle welfare and beef quality by minimising stress with the aim of improving consumer satisfaction with Australian beef.
Goals
• Identify potential gene markers for adaptation, stress perception and activation of the stress response
• Evaluate methods for assessing cattle temperament by demonstrating their relationships with measures of the stress response, cattle performance and beef quality.
• Quantify the individual variation in the stress response (behavioural and physiological) of cattle to specific stressors that influence beef quality.
• Develop methods to enhance the adaptability of cattle to stressors encountered during production.
• Develop alternative pre-slaughter (on-farm, transport and lairage) management practices that minimise stress in order to maximise beef eating quality and animal welfare.
• Integrate the outcomes from the above objectives into systems designed to improve cattle welfare and beef quality.
Strategies and Progress
There was limited activity within the project during 2005/06 as the majority of the research had been completed in the previous year. The primary focus during 2005/06 was the completion of the two post-graduate student research activities and the submission of scientific manuscripts. Kelly Drake and Lysandra Slocombe concluded their experimental work and are now in the process of completing their theses. Three journal manuscripts were accepted for the Meat Standards Australia special edition of the Australian Journal of Experimental Agriculture. These manuscripts were specific to the research which was undertaken as part of Strategy 2.4.3 ~ Optimal Pre-slaughter Management of cattle to maximize beef quality and welfare. A further 5 manuscripts from other strategies are currently in preparation and will be submitted in 2006/07.
Project 3.3 ~ Regional Beef Systems to achieve market specifications
Mission
To use combinations of genetics, nutritional pathways and best-practice management across regional Australia to improve market compliance and hence product value.
Goals
• To develop strategies that will prepare cattle for live export and improve on-board nutritional and environmental conditions
• To test and validate combinations of genetic, nutritional pathways and best-practice management to increase the proportions of cattle achieving market specifications across regional Australia
• To develop and validate nutritional strategies which allow for the efficient utilisation of feed resources (including feed gap problems) to improve target market compliance.
Strategies and Progress
This project was designed to elicit and foster cooperative arrangements between the various State Departments of Agriculture across Australia to deliver appropriate beef cattle research and extension to producers in regional Australia. The research is of an applied nature responding to beef producers’ perceived requirements within a regional context and yet with Australia-wide implications. Because of its regional focus, cooperative arrangements were also forged with producers, producer companies and various meat processors to facilitate local ownership and uptake of results.
Nutritional treatments were imposed on a range of cattle genotypes to create divergent growth pathways to identify the best combination of genotypes for a given production and management system.
Sires with accurate EBVs for carcase type (yield, yield and marbling, marbling) were chosen to optimise chances of generating appropriate progeny groups. Sires used in previous
Sub Program �. Delivery of Technologies to the Beef Business System
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CRC studies were specifically chosen to provide linkages to past studies and between Regional Combination sites to increase the power of the experimental design. Standardised meat quality sample collection and testing protocols were used at each site. Each site’s results will be individually analysed and an across site analysis will follow allowing a better evaluation of the influence of environment. A standard economic evaluation process has been agreed by collaborating economists in Victoria, Western Australia and NSW.
Four research sites in NSW, Vic, SA and WA with a clear common focus were established, resulting in the collaboration of 4 state Departments of Agriculture, various Universities, industry co-operator/producers and major meat processing works – covering all stakeholders in the beef production chain. Progress in 2005/06 included:
• All sites have now completed experimentation and collected all usable data.
• Meeting was held in February 06 to finalise consistent approach to within site biometrical and economic analysis.
• All data entered onto the CRC database.
• Across site genetic analysis to be conducted by AGBU.
Results thus far indicate that carcase type has a major impact on the ability of cattle to meet variable and exacting market specifications.
Market specifications can be defined as incorporating market requirements for weight and fatness, eating quality and meat yield. Important findings regarding comparison of carcase types
to date indicate the high yielding types can satisfy all criteria and add value to the end product in terms of increasing total quantity of an acceptable product.
The combination of particular carcase types will most certainly increase market compliance and improve herd profitability particularly as the beef industry moves towards a true value based marketing system.
In terms of nutritional pathways, there are indications of interactions occurring between growth rate, finishing regime and expression of carcase quality attributes. These data have the potential to reveal new evidence in assisting producers to better meet market requirements through manipulation of cattle growth paths.
Information is being generated at both the Western Australian and the Victorian sites in regards to best management practices for calving time relative to these particular environments. Clearly in both instances weaning weights and hence profitability was enhanced by selection of a more appropriate time of calving.
Project 4.4 ~ Integration and Delivery of CRC Technologies and Information
Mission
To facilitate adoption of the CRC outcomes by the beef industry.
Goals
• Distil research outputs into intelligent business solutions.
• Develop and deliver integrated training packages for temperate Australia.
• Develop and deliver integrated training packages for sub(tropical) Australia.
• Participate in major industry events.
Strategies and Progress (Temperate Australia)
1. Awareness actvities
• The book “Producing Quality Beef ~ Opportunities for Beef Producers from the CRC for Cattle and Beef Quality” was reprinted in November, 2005, with 3,000 copies printed. They have been distributed to CRC stakeholders across Australia at Field Days, meetings and via mail request.
• Production of new publication in conjunction with MLA on the new Australian Beef Carcase Appraisal System (ABCAS) which incorporates CRC and MSA technology into beef carcase assessment.
• MSA awareness via the ABCAS system - the project was involved in the development, trialing and implementation of the new ABCAS at Sydney Royal Show in April, 2006 and Beef Australia 2006 at Rockhampton in May, 2006.
• MLA Edge Effective Beef Breeding Workshop - the project contributed to development of the revised Effective Breeding Edge workshop, incorporating latest Beef CRC results, and presented a pilot workshop at Armidale in May, 2006.
Sub Program 4. Education and Training for the Beef Business
Weighing a calf as part of the research for Project 3.3
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• ProFarm Beef Breeding Extension package - the project commenced development of a 2-day ProFarm Beef Breeding Extension course, using a “proof of profit” case study approach to demonstrate the benefits of adoption of beef genetics technologies. CRC results were incorporated into the content of this course.
2. Engagement activities
• CRC Field Days - “Wean More, Grow More - Better Beef “ CRC Field days were conducted at Holbrook (90 participants) and Carcor (90 participants) in March 2006, and Bungendore (85 participants) in June, 2006.
• Integration of CRC results into MLA More Beef from Pastures - CRC genetics, growth path and meat quality results were integrated into More Beef from Pastures Train the Trainer workshops for consultants and workshops were presented at Tamworth, Wagga Wagga, Hamilton (Vic) and Busselton (WA).
• CRC Breeding Update Workshop for Extension staff - the project sponsored an intensive 3 day breeding and genetics workshop conducted by AGBU staff at Tamworth in November 2006 for Beef Extension staff from NSW and Qld DPI, including comprehensive coverage of CRC genetics results and their application in breeding extension activities.
• Armidale, Feeder Steer School - A highly successful Feeder Steer School was conducted at Armidale in February 2006 in conjunction with the Angus Society, with 90 participants. As in previous years, this school focused on the practical application of CRC technologies in commercial breeding and growing enterprises.
• Southern Beef School - project presented CRC results at the Southern Beef School at Glen Ormiston, Vic in July 2005 in conjunction with Vic DPI and the Angus Society, with 80 participants.
• Tocal Cattle Assessment School - CRC results were presented at the Tocal Cattle Assessment School in July 2005, with 80 participants.
• BIA Conference Moree - CRC results (meat quality and feed efficiency) were presented at the Annual BIA Conference at Moree in July 2005 (250 participants).
• Moree Domestic Feedlot Supply Chain Workshop - A supply chain workshop was conducted in October in conjunction with Tallawanta Feedlot, Wilga Feedlot, Welcannah Feedlot and the BIA involving 60 producers.
• Other CRC presentations included US Composite Beef Breeders tour (35 participants); UNE Meat judging team (24 students); Alice Springs Benchmarking group (15 participants); Hunter Beef Producer group (25 participants); Glen Innes Intervet cattle producers evening (80 participants); MLA Insights Pilot Workshop for consultants (25 participants); Colorado State University group visit (25 participants), Brisbane Valley Beef producer visit (20 producers); Intercollegiate Meat judging students (30 students).
3. Training activities
• Training workshops were conducted in Tamworth and Wagga Wagga for
NSW DPI staff in the use of BeefNomics package for focus group activities. Pilot CI & I workshops were conducted at Glen Innes, Yeoval and Tarcutta using BeefNomics and CRC technologies as the focus for “what-if” scenario analyses with producers.
• 25 BeefNomics groups, comprising 265 producers, have been planned and/or initiated in NSW, using the BeefNomics training package (course modules and software) as the focus for considering the impact of technology adoption. The groups are widely dispersed throughout NSW, including Glen Innes, Inverell (2), Tamwoth, Manilla, Holbrook, Hartley, Dunedoo, Coonabarabran, Warren, Trundle, Mandurama, Moree (2), Yanco, Adelong, Paterson, Dungog, Bega, Berry, Golburn, Cooma, Taree (3). These groups are in various stages of development and will form the basis of Beef Profit Partnership groups to be conducted in Beef CRC III.
Strategies and Progress (Sub-tropical Australia)
The DPI&F Commercial Application of Beef Genetic Technologies (CABGT) team have continued to conduct activities to:
• Increase awareness of all the Beef CRCs and their outcomes; and
• Increase adoption of technologies developed from CRC research by packaging the information for regional beef production systems in northern Australia.
The following activities occurred in 2005/06:
• “Train the Trainer” workshop
• BREEDPLAN workshop - The major focus of the workshop was CRC outcomes as they apply to BREEDPLAN technology.
• CRC industry training and CRC outcomes
Using group participation and adult learning principles, these days have introduced industry participants to the CRC and outlined a suite of technologies and information including how it can be applied to improve enterprise profitability. Workshops were held at 7 location son the Darling Downs.
In addition a further 10 workshops were presented to beef producers in New Zealand in conjunction with Meat and Wool New Zealand. M&WNZ are Participants of Beef CRC III so this was an opportunity to develop relationships with producer groups involved in the next phase of the CRC.
Other practical activities were initiated as follow-up activities, including:
• Flight time measurement of animals involved in a Whole Cottonseed trial at Texas (8 participants)
• Measurement of flight time on weaners at “Politic”, Aramac (23 participants)
Optimal HerdExpansion
PV($ x 106)
Year-25 Stock No.s(br/ha)
Deterministic – base herd Steady state 1.2864 0.96Deterministic – NFI herd +6.2% 1.3182
(+ 2.5%)1.02(+ 6.3%)
Stochastic- base herd Steady state 0.9129 0.81Stochastic- NFI herd +2.4% 0.9417
(+ 3.2%)0.83(+ 2.5%)
* Indicates percentage change compared with the respective deterministic or stochastic base herd model.
Table 1. Optimal herd expansion with NFI under deterministic and stochastic pasture assumptions
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• Bull Selection Workshops - Seven workshops were conducted across the state. The workshops ensure producers understand that bull selection is an important tool influencing within herd genetic improvement. CRC outcomes including docility measures, marker assisted selection and the use of BREEDPLAN are integrated into the workshop package.
• Breed Society Activities - activities with tropical breed socieities including Droughtmaster and Belmont continue.The improved linkage study involving eight Droughtmaster herds (Swans Lagoon, Lisgow, Home Hill, Rewan, Clonlara, Glenfosslyn, Old Man Plains - NT DPI FM Alice Springs and UQ Veterinary School) has progressed well. Docility measures, DNA marker information and carcase scan data have been collected for analyses. The Belmont society recently included Days-to-Calving EBVs in their BREEDPLAN analysis to assist with selection for fertility traits. BREEDOBJECT and an animal enquiry facility on the web-site has also been introduced.
AAABG
• QLD hosted the 16th Biennial Association for the Advancement of Animal Breeding and Genetics (AAABG) Conference.
• A regional tour of QLD followed the conference attracting ~150 producers from central and southern QLD to the post conference Beef Industry Breeding seminars.
• These seminars were coordinated and chaired by the CABGT extension team and attracted significant discussion from supply chain participants on how these latest technologies could be applied to their respective businesses.
EDGEnetwork
The first EDGEnetwork - Breeding workshop was conducted at Kingaroy for seven enterprises. Subsequent workshops which incorporate CRC outputs have been conducted in Katherine, NT and Aramac, Qld for a total of 39 participants.
Participants of the Kingaroy workshop have engaged in a follow up day to refine the breeding plans developed for their enterprises. Follow up activities are planned for the other workshop groups and a 4th Breeding Edge workshop is being organised for late July 2006 in Mundubbera.
CRC information including growth paths, compensatory growth, HGPs and docility was presented as part of the EDGEnetwork - Nutrition workshops presented around Queensland.
Student education – Undergraduate and vocational
• Australian Agricultural College Corporation training the CABGT team completed 4 weeks of training for >70 students of the Emerald Campus for Diploma 1 and Diploma 2 students in the cattle breeding program during 2005-2006. Practical activities and projects completed by these students included: Bull Breeding Soundness Evaluation on yearling bulls; measures of docility including flight time and crush test; and collection of DNA samples for analysis of the frequency of the tenderness and marbling markers.
• University Queensland Pastoral Veterinary Centre - A basic overview of genetic evaluation systems, principles behind BREEDPLAN values and the new CRC for Beef Genetic Technologies was presented to 48 fifth year veterinary science students.
Major industry workshops
• Feeder steer schools / Emerald Beef School - In July 2005, a beef school was conducted that attracted ~ 25 delegates. Each participant received a comprehensive overview of the issues facing Queensland beef producers. Topics included markets, live assessment and genetic improvement programs.
Project 5.5 ~ Economic Impact Assessment Project
Mission
To develop and apply best-practice economic analysis modelling systems that provide sound advice to CRC management and all participants in cattle and beef production and marketing about expected returns from investments in new technologies.
Goals
• To collect, evaluate and where appropriate, integrate existing models of various aspects of the beef production and marketing system in different regions of Australia to form a suite of models for different levels of analysis
• To undertake research to enhance the capabilities of this suite of models and to update the input data sets used in these models so as to maintain a close relationship between changes in industry structure and operation and evaluation outputs
• To support management by providing data and commentary on the economic impact on the Australian beef industry of both completed and proposed scientific research programs and projects
Strategies and Progress
The CRC invests significant resources in developing new technologies. The aim of this project is to develop and apply best-practice economic analysis modelling systems that provide sound advice to cattle producers and other participants in beef production and marketing about the expected returns from these investments. The work in this project during 2005/06 involved economic analyses of the experimental data arising from several projects in the CRC.
Economic evaluation of the Grafton trials (Project 1.1/1.2). All experimental data analyses for this project are now complete and were released in March. Initial evaluation of the data has commenced using the Beef-N-Omics software program that incorporates feed budgets and financial gross margin budgets for cattle herds. This model allows for the input of various ages and live weights for growing stock from weaning to turn-off. Initial modelling of the various pastures and cow/calf growth profiles for the various treatments has been undertaken to identify similar pasture growth profiles provided in the Beef-N-Omics pasture library. Various prices including abattoir price grids and variable costs including pasture and feed costs have been collected. Preliminary results have been generated for discussion with project staff.
Sub Program 5. Administration: Beef Research in a Business Environment
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Further economic evaluations of the Net Feed Intake research (Project 2.2). A bio-economic model of a Northern Tablelands cattle grazing enterprise was specified and validated, and used to re-evaluate the economic efficiency impacts of the adoption of NFI under both deterministic and stochastic pasture growth functions. The main results are reported in Table 1, in terms of present value (PV) of the herd gross margins over 25 years, and the number of breeding cows per ha (br/ha).
The adoption of the NFI technology in this representative herd using stochastic pasture growth indicated a 3.2% improvement in PV over the respective unimproved herd scenario, after accounting for the cost of forgoing heifer sales and the changes in feed requirements and cash flow as the herd expands. This is equivalent to about $5.30 per cow per year. The optimal herd size rose by 2.5%. Investment in the NFI cow herd was found to increase as the profitability of the beef enterprise decreased, and as the initial level of genetic improvement in the NFI trait increased.
Adopting the NFI trait also has the potential to reduce enteric methane output in the range of 11% to 20% per animal after 25 years. Simulations accounting for differences between Northern and Southern production systems indicate that over 25 years a cumulative total of 568 Gg of methane would be abated. A minimum value for the saved methane output due to the adoption of RFI genetics in the national beef herd is estimated to be $125.3 million.
Economic evaluation of Project 2.3.1. A 2-day workshop was held in Darwin in July for the economists and a number of technical people representing the various northern environments to outline the BreedCow program and its data requirements and to make progress on these evaluations. A number of representative farm models were decided on and some preliminary gross margin analyses were done to test the models that were available. Further progress has been made to complete those models that were unavailable at that stage. Further work on these analyses depends on completion of the statistical analysis of the experimental data.
Economic evaluation of the South African work (Project 2.3.3). Economic input into the current South African ACIAR project was maintained. The project leader visited South Africa as part of the ACIAR final project review and commenced an economic analysis of the project outcomes. He also participated in meetings and discussions relating to a proposed follow-up project that will be linked with CRC III.
Economic evaluation of the MSA and beyond project (Project 3.2). Following the completion of an MLA survey that measured premiums for a range of MSA cuts across different cities and in different parts of the chain, an evaluation of the aggregate returns to the MSA program was completed. Based on records of the number of carcases graded as MSA and the calculated premiums from the survey, this analysis estimated that the cumulative retail value of the MSA system to 2004/05 is $159m (in terms of 2005 prices), with a projected benefit of almost $85m for the 2005/06 year. Given total costs of the R&D and the subsequent development of the MSA system of about $82m to date, the ex post benefit-cost ratio therefore is in the order of 2:1, to date.
Economic evaluation of the regional combinations trials (Project 3.3). A 2-day workshop was held in Adelaide in August for the economists and the four site technical directors to outline the Beef-N-Omics program and its data requirements and to make progress on these evaluations. Further work on the economic analyses depends on statistical analysis of the experimental data. However some preliminary gross margins for the “fast” vs “slow” growth treatments in the southern NSW site have been calculated, based on a 100 cow herd and averaged across all breed types (Table 2). There is a potential 3% improvement in gross margin from adopting nutrition and management strategies to achieve market specifications faster.
Table 2. Gross margins per hectare by growth rate
Finalisation of the remaining economic evaluations for CRC II will occur when the final statistical analyses of project 2.3.1 and project 3.3 are completed. These will be done within Program 5 of CRCIII.
Treatment Total Gross Margin Gross Margin per Hectare
Slow $37,627 $188.13
Fast $32,969 $193.94
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Research Collaboration - CRCIII
> Research Activities and Achievements
> Program 1
> Program 2
> Program 3
> Program 4
> Program 7
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Research Activities and Achievements
Key research achievements for Year 1 of the CRC for Beef Genetic Technologies (CRCIII*) include:
• A whole genome scan for MQ4 (eating quality) scores was performed on CRC1 cattle in November 2005. Genotypes were received in December 2005 and candidate genes are being pursued.
• Preliminary results from Angus cattle divergent in muscling and yield characteristics suggest the establishment of a breeding program targeting one non-functional myostatin mutant allele (heterozygotes) can increase retail beef yield by about 3.5% with no adverse effects on eating quality.
• Secured agreement on international co-operation and commitment to a collaborative approach on biological models for prediction of phenotype.
• Whole genome scan of Trangie NFI cattle was completed, and candidate genes for feed efficiency are currently being pursued.
• 120 cattle from the Trangie (NSW) NFI selection lines were relocated to Vasse (Western Australia) to commence maternal productivity studies.
• Sources for isolates of methanogenic archaea representing the four major phylogenetic groups (of rumen micro-organisms) have been identified.
• Batch and semi-continuous culture systems and corresponding gas analysis systems have been developed to monitor methane production.
• Materials transfer agreement between USDA (tick genome resources) and QLD DPI&F and Murdoch University was signed and unpublished tick sequence data were transferred to Beef CRC.
• 600 Brahman females were chosen for an age of puberty whole genome scan and the genotype information was received at the end of March 2006. Analysis of the data is currently underway.
• Genetic parameters were estimated for:
All 2005/06 milestones have been met, and at this stage no major changes are proposed to the future direction of the CRC. The CRC was not involved in any major consultancy. In addition to the Commonwealth CRC grant and the participants contributions, the CRC was awarded a 4-year grant of $300,000 by the Qld Department of State Development, Trade and Innovation. The grant is for the development of a commercial DNA test to improve reproductive rates of tropically adapted cattle (CRCIII Project 4.1.1).
Research in the CRC for Beef Genetic technologies is in its early phase, however the planned outcomes will be in alignment with
the National Research Priorities thus:
• Frontier Technologies for Building and Transforming Australian Industries – through application of genomics, proteomics and bioinformatics technologies to understand and utilise the genes controlling basic biological processes in cattle to profitably meet the exacting demands of our global beef markets.
• Promoting an Innovation Culture and Economy in the Australian beef industry by using novel partnership strategies to reduce the ‘Research to Adoption Cycle’ from 5 years to 2 years.
• Protecting Australia from invasive diseases and pests by using cattle genetically more resistant to parasites.
Outcomes (as per Commonwealth Agreement)
• By 2012, a comprehensive genetic improvement package that incorporates genomic and other animal breeding technologies for the genetic improvement of carcase yield, marbling and beef tenderness in commercial cattle being used by industry to increase annual gross revenue of the Australian beef industry by $43m for improved beef quality and a further $15.5m for increased retail beef yield.
• By 2012, a sector-specific individual animal performance prediction system for growth and carcase characteristics that includes EBVs, DNA tests and gene expression data that is being used by industry to result in a 20% increase in compliance of individual cattle to carcase specifications.
• By 2012, palatability prediction models with specifications for international markets will be used by Korea and Europe to satisfy their consumer demands for guaranteed eating quality.
The outcomes in Program 1 will be addressed by the following projects.
Project 1.1.1/2 Full utilisation of genetic markers for improved beef quality
Improving the genetics of meat quality is difficult because the animals used for breeding are not directly measured for the trait. DNA testing is one possibility to understand the genetics of meat quality.
To date, 4 DNA tests based on 3 genes have been licensed for testing for meat tenderness in Australia, which leads the world
Research Collaboration - CRCIII
Program �. High Quality Beef for Global Consumers
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in this technology. The range of meat tenderness explained by these markers is approximately 0.5kg of shear force, which is close to the “Bos indicus” effect on meat tenderness. There are 4 DNA tests based on 4 genes licensed for testing for marbling around the world, and the range of marbling is around 0.7 of a marbling score. Although these differences are very useful, they represent less than half the genetic variation for these traits, which means there is still substantial improvement that can occur in these tests.
The main aims in this project are:
• to identify at least 50% of the genetic variation for marbling, tenderness and retail beef yield using DNA markers
• to commercialise these DNA markers so that they are offered as genetic tests, and
• to test DNA markers identified in other countries and evaluate them on Australian cattle to see how well they work
Strategies and Progress
The team completed a preliminary study, which aimed to identify a very large part of the genetic variation behind meat tenderness. They identified at least 20 promising DNA markers, testing more than 9,000 DNA markers to achieve this, within the milestones set for the project. The measurements were consumer taste tests of beef tenderness, so the results have a direct impact on what the consumer perceives as high quality beef. Researchers usually use shear or peak force measurements to measure tenderness, so using consumer panels to assess meat quality makes this a ground breaking study with potentially unique results. It required the CRC’s large DNA banks and databases already collected married to the latest molecular genetic technologies. The team will expand these preliminary results in larger samples, which will represent a wider range of sires, breeds and market endpoints, to confirm the results before any of these markers could appear as commercial tests.
Having DNA markers to predict the genetics of the animal is one goal, but another goal is to try to understand how the markers work. If we know how the markers work, then we can be sure that we are dealing with the correct genetics, rather than working with the genetics that only seem to be right. To do this, we need to study in detail animals of known genetics for the DNA tests. This has not been done in any great degree before
for these meat quality tests in any country, so in this regard the CRC is at the forefront of work in this area. This year we have genotyped more than 1,500 animals for the 4 current genetic tests for meat tenderness and selected animals that have 0, 1 or 2 copies of the favourable forms of the gene, and mixed and matched a group that has enough animals of each combination to make a scientifically useful collection. The research team in project 1.1.3 will study these animals further.
In the coming year the team will begin preliminary studies of retail beef yield and intramuscular fat using more than 30,000 starting DNA markers to identify promising DNA markers for further study. In addition, we will seek out animals that vary for DNA markers for intramuscular fat to better understand the way intramuscular fat is deposited. The ultimate goal here is to understand the trade-off between lean growth and fatness, and the constraints in certain segments of the market. We will also begin a major study of how DNA markers contribute to Supply Chains working with Project 1.2.2.
Project 1.1.3 ~ Proof of Concept
The overall goal of this project is to provide biological and metabolic proof of concept for meat science and carcass compositional gene marker effects on phenotypic outcomes. It has become clear that discovery of SNPs and QTL alone will not be sufficient to develop and implement novel gene-based technologies. Technologies that seek to predict or even determine animal phenotype, will increasingly depend on a thorough understanding of the metabolic pathways underpinning phenotypic variance. This understanding will also help to avert unwanted or unexpected effects of marker-assisted selection, for example, due to antagonisms between increased meat yield and tenderness or marbling.
The aim is to hypothesise and then verify scientifically, mechanisms that account for genetic variation in these traits so that discovery of new SNPs and new markers might be
Muscling genotypeVariable Low, wild-type (Lwt) High, wild-type (Hwt) High, heterozygote (HHet) s.e.d.Number of cattle 19 14 11 -Liveweight (kg) 666 659 638 24.1Carcass weight (kg) 359 360 357 13.5Rib fat (mm) 18.7 16.2 16.4 1.77Eye muscle area (cm2) 70.4a 76.9b 85.0c 3.05AUS marble score (0-6) 1.32 1.13 0.92 0.20MSA marble score (100-1100) 329 324 288 24.3Retail yield (kg) 218 221 234 8.5Retail yield (% CCW) 61.8a 63.0a 66.5b 0.68Longissimus shear force (kg) 4.70b 5.11b 3.98a 0.348Mean values followed by different letters differ at P<0.05. CCW, cold carcass weight.
Table 1. Least squares means for liveweight, carcass, yield and eating quality characteristics of low and high muscling Angus steers at 25 months of age and equivalent carcass weight (358 kg) where appropriate.
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strengthened through aspects of a “candidate gene” approach. Mechanistic knowledge will allow us to further develop industry strategies to improve phenotypic traits by targeting axes that control expression of the traits. Furthermore, this knowledge may also allow us to develop other means to the end: production of more meat of high eating quality, and an example might be a production vaccine.
Understanding the biological mechanisms through which suites of gene markers influence phenotype will effectively:
• Enhance industry confidence to embrace gene marker technology;
• Support our prediction of pathways (genes, proteins, or enzymic networks) through which environmental factors might influence phenotype;
• Help us uncover new technological options for influencing phenotypic expression, such as timed nutritional interventions and, perhaps, vaccines and pharmaceuticals;
• Contribute to the discovery of new genes involved in meat and carcase quality
Strategies and Progress
In conjunction with Project 1.1.1/2, gene markers for calpastatin, calpain 1 and/or calpain 3 will be the primary focus of a tenderness experiment to be conducted in 2006/07. The experimental design will also incorporate effects of HGP, sex, method of hang, and specific commercially important muscles. Phenotypic data and tissue samples were collected from Angus cattle divergent in muscling and yield characteristics.
High muscling Angus steers heterozygous for a myostatin mutation produced less fat and bone and more beef at an equivalent carcass weight, and had greater eye muscle area, than wild-type High and Low muscling Angus selection-line cattle (Table 1). Results suggest the establishment of a breeding program targeting one non-functional myostatin mutant allele (heterozygotes) can increase retail beef yield by about 3.5%, with no adverse effects on eating quality. Analyses to complete objective eating quality and muscle cellular characteristics are continuing for semitendinosus and/or longissimus muscles.
An initial review of factors influencing marbling was undertaken and published for industry to provide a platform from which a more detailed review of influences of nutrition in early life, effects of specific substrates, and depot-specific substrate utilisation will be undertaken.
Project 1.2. Prediction of phenotype
To assist producers to make more informed management decisions and to increase the proportion of cattle which meet market specifications, models are required to predict performance of individual animals. These models need to predict growth during the finishing period (for both grain and pasture) to achieve a carcase end-point and carcass traits at slaughter (both yield and quality). The model should eventually incorporate the current MSA model and a simple growth model. The simple growth model combined initally with, gross genotype effects, and then sequentially specific genotype effects, will allow prediction of animal’s carcase performance in meeting both specifications and eating quality.
This project will incorporate initially growth traits, environment and breed as inputs into existing and new growth models to predict growth and carcass traits of individual animals. As the project progresses, EBVs and gene markers will also be included as inputs into the models. If this results in satisfactory levels of accuracy, these models will be used to increase the proportion of cattle which achieve specifications. From an industry viewpoint, some form of modelling of sophisticated traits and their interactions with other traits is required to simplify the process a producer/breeder/fattener needs to undertake to select animals for a particular purpose and market end point. The phenotypic selection process via these models will be well linked to the genetic index selection tools currently available through BreedPlan, allowing for a continuum of selection direction.
Strategies and Progress
Model identification and development:
Tasks for the first year or two of this project were broken into four components:
1. Evaluation of simple models.
a) Evaluation of a model that estimates “maturity type” based on fatness of calves at a given weight and age. This could also be termed “residual fatness” based on the following model:
Fat depth = m + b1(weight) + b2(age) + residual
Taking these parameters (m, b1, b2) from earlier growth (e.g. pre-feedlot), maturity type (MT) has been shown to be repeatable over a range of ages. Specifically, if the residual term = MT, then fat depth can be predicted based on age, weight and maturity type.
The aim of the first stage is to test the robustness of this model. This will include repeatability of residual fat as well as using the model to predict fatness at a range of ages.
b) A model from the Australian Feeding Standards manual (termed the SCA model or “composition of gain”) is being evaluated and further developed in association with a market specification analysis system to more accurately evaluate an animal’s ability to meet market specifications (an integral component of the concept of a final model). The major data set for this work (CRC2 Regional Combination data) will be complete by June 2006 and full specification analysis on all sites complete, allowing this to be incorporated into further prediction models.
c) The project is now funding a masters student to analyse a unique MSA carcase dataset (small supply chain network with very comprehensive and accurate data). This will assist us in the “Market/End Point” component of the model and in testing to determine accuracy of prediction or achieving, based on meat quality and yield as an end point.
2. Data sets.
Evaluation and specification of data sets is currently underway with the Australian data sets including CRC 1 and 2, Southern Crossbreeding data, NSW DPI data of Trangie growth, Grafton Crossbreeding and EMAI muscle.
3. Converting units to market components.
The intention is to ensure that phenotypic outputs are expressed in units that are both useful to the end purpose
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and common between models. This entails converting units/measures between existing models, so that outputs from different models are comparable by converting terms such as total protein to total carcase muscle, which is more useful for most cases other than biological models; and turning genetic and nutritional parameters into phenotypic animal descriptors for inclusion in developed models.
• EBVs for relevant traits (RBY, IMF) into phenotypic measures that equate to phenotypic expression of that trait (eg kg) at specified stages of production chain.
• Nutritional measures (intake) to growth rates
• Growth rate units to units of wt, fat, yield at specified stages of the production chain
• Nutritional measures (quality) to composition of gain (eg. units wt, subcutaneous fat, fat depth, IMF)
4. Evaluation of appropriate models:
The purpose of the model evaluation work is to find what’s been done before to bring together nutrition and genetic inputs that contribute to prediction of phenotype, test to see how they can inform the activities in the project and what data and computational needs are required to predict phenotypes of Australian cattle. Models that might be included in the evaluation include those available from USDA, UC Davis, the Australian scene generally (ranging from SCA and BreedObject) and elsewhere. The project is currently communicating with many researchers across the world to progress this phase of the project.
Supply Chain Validation for Performance Prediction Models
In this program a number of technologies are being developed to assist beef producers to turn off cattle that better meet market specifications. They include the identification of gene markers for tenderness, yield of saleable meat, muscling, marbling and fatness. These gene markers are being identified by use of information from cattle in previous CRC studies. The size of effect of these genes will need to be quantified using a sample representative of the current cattle population.
The program is also making use of historical databases to develop models designed to predict performance of individual animals at various stages in the supply chain. These models will be aimed at selecting animals that have the best chance of meeting specifications for weight/fatness as well as meat quality, marbling and yield of saleable meat. They also need to be tested, validated, refined and packaged in a form that is readily useable by beef producers.
Implementation of technologies in the beef industry has traditionally been slow compared to other intensive livestock industries. In this CRC, the principle of accelerated adoption is being employed to address this problem. This involves the formation of small producer groups, (Beef Profit Partnerships) that focus on profit and operate by measuring current performance and setting of targets for future productivity and profitability increases. The process of measuring and evaluating will be undertaken at regular intervals with progress monitored using cost of production and gross margin analysis. In this program the producer groups will be formed in association with a beef processor and the focus will initially be on improving carcase characteristics and compliance to market specifications.
The key to improving compliance to specifications and carcase value lies firstly, in an effective feedback system to the producers, and secondly, in the implementation of suitable technologies by producers. The first step is to collect and critically analyse objectively measured data on groups of slaughter cattle. It is only when the strengths and weaknesses in the carcase characteristics are identified and recognized that actions can be taken to improve. The methods of objectively measuring performance of most characteristics are available through the AUS Meat feedback data and the MSA grading system. These three sets of data provide all the information that is necessary to determine how well animals comply with specifications and their value for a particular market.
These data and analyses firstly need to be communicated to the producer in a form that can be understood. Secondly and most importantly the data need to be interpreted in terms that allow the producer to decide to adopt some of the range of technologies that are available. Research and extension personnel will forge collaborative links with producers and processors in these supply chain Beef Profit Partnership groups and will assist with providing technical information as well as facilitation of the group process. The target is to form at least 5 supply chain groups in Qld, NSW, W.A and N.Z.
Quantifying of the effects of DNA markers will make use of producers involved in the supply chain networks. For this study DNA and meat samples will be collected from a large sample of cattle from the cooperating supply chains. A methodology has been developed for the collection, over the next 2 years, of samples from 2,500 animals of many sire lines within a wide range of breeds. While use in gene marker studies for tenderness is the primary use for the sample, it will also be useful for benchmarking other quality traits such as fatness, marbling and meat yield in supply chains
Once prototype models have been developed they will be made available initially to producers within the supply chain networks where they will undergo extensive testing of their usefulness. This may lead to further development and modification to the models.
Outcomes (as per Commonwealth Agreement)
• A comprehensive genetic improvement package that incorporates genomic and other animal breeding technologies for the genetic improvement of feed efficiency in seedstock cattle.
• New knowledge and tools adopted by industry to enable the simultaneous improvement of maternal productivity, feed efficiency and end-product traits.
• A 5-10% increase in dietary energy captured by 50% of feedlots and 20% of grazing enterprises by 2012 through adoption of feeding and management strategies to reduce methane generation by 20%.
The outcomes in Program 2 will be addressed by the following projects.
Program �. Feed Efficiency, Maternal Productivity and Responsible Resource Use
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Project 2.1. Genetic improvement for feed efficiency
Research Outputs
2.1.1 A suite of DNA tests that explains 50% of the genetic variation in feed efficiency in cattle.
2.1.2 A comprehensive information package to underpin the commercialisation of the suite of tests for feed efficiency.
2.1.3 Knowledge about gene expression for feed efficiency at the molecular and animal levels, and the environmental and nutrition controls generated and incorporated into Breedplan and CRC Knowledge Base.
Strategies and Progress
Research by the CRC over the last decade has catapulted Australia to the forefront of R&D into feed efficiency of beef cattle with the outcome that the Australian beef industry has unique access to Estimated Breeding Values (EBV) for feed efficiency, to the envy of our major international competitors. Achievement of just modest rates of adoption of genetic improvement in feed efficiency is conservatively estimated to have a net present value exceeding $200M. However widespread industry adoption is hampered by the high cost of identifying genetically superior animals.
An affordable panel of DNA tests that explains 50% of the genetic variation in feed efficiency is required. These tests will become very valuable commercial property for use in Australia and sale internationally.
Net feed intake (NFI) is a trait where we expect to find many gene markers, but each of modest effect. The divergent lines for feed efficiency developed at the NSW Trangie Agricultural Research
Centre are the best resource available in the world for this purpose.
Some NFI gene markers were identified in the University of Adelaide Jersey x Limousin herd. Whole genome scans were conducted using the ParAllele SNP genotyping system on high and low efficiency cattle sampled from the Trangie feed efficiency herd and CRC1 herds. Results from both scans were compared and candidate genes chosen for subsequent evaluation. Panels of genes from each of three projects are the subject of provisional patent applications. These activities were conducted as CRCII Year 7 activities.
The work to locate specific genes is continuing using the Trangie herd. To generate cattle that are genetically
even more divergent for NFI, the divergent NFI-selection lines have been re-created using stored semen from high and low efficiency bulls. AI matings were conducted in 2004 and another generation of divergent selection progeny was produced. Another AI mating was conducted in 2005 and in 2006 another generation of divergent selection by natural service will be undertaken. Male and female calves will to be tested for postweaning NFI to provide the phenotypes required for gene detection.
Approximately 10 major metabolic pathways have been identified that are likely to be involved in net feed efficiency in cattle. From the initial QTL analysis, six of these pathways could still impact the genetics of NFI. To narrow the search for the candidate genes themselves, the role of these pathways in NFI must be elucidated. By examining the activity of these pathways in animals divergent for NFI, the importance of some pathways may be eliminated and/or the significance of other pathways may be validated, thereby reducing the number of potential candidate genes. The remaining candidates can then be analysed more closely for their association with NFI.
Preliminary candidate pathway experiments involved a series of small studies aimed at determining the potential role of at least 3 pathways in NFI. Muscle and liver samples were taken from commercial animals with a known range in NFI, and enzyme activities and mitochondrial function examined. Steers were derived from the Angus Elite Sire Progeny Test, following 70-day NFI test at “Tullimba”, harvested at Beef City abattoir in Toowoomba April 2005. Mitochondrial proteomics used 2-dimensional gel electrophoresis (a method for separating proteins by charge and mass) and, after image analysis, 960 protein spots were found. Out of 960 spots, 60 spots showed
Angus cattle at Vasse Research Station, southern WA.
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up and down regulation in tissue samples from high and low NFI cattle. To verify these and other candidate biochemical pathway differences, additional samples have been collected from low and high NFI Angus steers from the Angus Elite Sire Progeny Test, following 70-day NFI test at Tullimba, harvested in May 2006.
Project 2.2. Simultaneous improvement of maternal productivity, feed efficiency and end-product traits
Strategies and Progress
Knowledge of the mode of action of new gene tests and phenoptypic and genetic associations with all commercially-important production traits will be needed to underpin adoption. Most of the NFI research to date has been done with cattle being fed ad-libitum. How genes for improved NFI are expressed in animal production systems when the animals are fed below ad-libitum (typical of pastures most of the year) is not known. Do differences in feed efficiency reduce or become more important? Are associations with growth and body composition, that are not strong on ad-libitum feeding, more strongly expressed as feed availability declines, and are they favourable or unfavourable?
These relationships will be investigated across a range of environments and nutritional regimes in temperate areas of Australia. Key components of maternal productivity to be examined include cow feed requirements, reproductive performance, calving ease, calf value, cow survival and cow salvage value.
The efficiency and maternal productivity of the breeding cow has a large influence on the efficiency of the entire beef herd. The feed requirements of a cow just for maintenance comprises something like 75% of the total feed requirement of the herd. Thus targeting the feed requirements of the beef cow to reduce this cost will have a substantial impact on overall herd efficiency. Beef producers have embraced Breedplan estimated breeding values (EBVs) to change carcass characteristics (ie yield, fatness, marbling), and EBVs are now available to beef producers to select cattle on efficiency (or net feed intake - NFI). However there is little information on the effect of selecting for these traits on maternal productivity.
Maternal productivity is a function of fertility, dystocia, milking ability and calf growth. A starting point for this project will be mining and analyzing Breedplan databases to quantify genetic relationships between maternal productivity, feed
efficiency and body composition traits in varying nutritional regimes using a “reaction norm” approach. Phenotypic prediction models will also be developed in collaboration with Program 1 to aid management decisions for specialist beef producers.
However, Breedplan data sets are insufficient for quantifying maternal contribution, so additional measurements (primarily cow body composition) and facilitation of collection of existing records which are often poorly recorded (e.g. reason for culling) will be undertaken on progeny test herds and commercial properties. This will involve repeat (4) ultrasound measurements on a large number (6,000) of heifers/cows in selected Breedplan herds (4,000 Angus, 2,000 Hereford and 2,000 Shorthorn -including females involved in the Durham project). Females will have previously been scanned for EMA, P8 and rib fat, and IMF% as yearlings and will also have been sampled for IGF-1. They will subsequently be scanned and weighed pre calving (their first calving) and at weaning and also at their second calving and weaning. IGF-1 samples will be taken from the cows at each weaning. The females will be monitored for Breedplan maternal productivity traits (fertility, liveweight, calf performance and longevity).
In addition to research in cooperator herds, a comprehensive evaluation of breeding herd efficiency differences between genotypes divergent for NFI under various nutritional regimes (high versus low stocking rate) will be conducted. This will involve 120 heifers from each genotype for 3 joinings at Struan (SA) and Vasse (WA) research stations. Vasse has already taken delivery of their heifers and Struan will start in year 3 of the CRC. The research herds provide opportunities for intense measurements and demonstration sites as part of the industry adoption strategy.
Scanning cattle at Vasse Research Institute WA
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Project 2.3. Feeding and management strategies to increase dietary energy capture & reduce methane generation
Strategies and Progress
The overarching goal of this project is to alter the ecological and fermentative contexts of rumen microbiology, to reduce methane emissions and simultaneously improve feed efficiency in Australian beef cattle. To that end, integrated studies in (meta)genomics, microbiology and animal nutrition will be employed throughout the project. During the last year, DNA-based technologies were developed as part of a joint project between the Australian Greenhouse Office, the Australian Lot-Feeders Association, CSIRO and the CRC that will now be used to identify and characterize the microbial biology underpinning hydrogen utilizing pathways other than methanogenesis in rumen microbiomes. A cross-section of the methanogens resident in rumen microbiomes is also being assembled and will be examined at the DNA and protein levels, to provide targets for the development of novel classes of methanogen inhibitors. Bioactive materials that might be used to compromise the growth of ruminal methanogens will also be screened using these strains. Integrating these microbial studies with the whole animal studies that may be undertaken within Program 2 is vital to our success.
These microbial-based technologies and approaches will be integrated with some of the whole animal studies in Program 2 during 2006/07. Specifically, methane output will be measured in bulls from Trangie that are currently being measured for feed efficency at Tullimba feedlot. The aim is to identify “low emitters”. Thereafter the microbiomes of selected animals will be examined using the technologies described above and related (meta)genomic methods. Successful completion of these studies will provide the foundation necessary to transition from bench-level to whole animal studies, which will seek to establish the fermentative schemes necessary to reduce methane emissions, and improve feed efficiency in beef cattle.
Products that may arise from this research include inoculants, bioactive agents and supplements that can be used to compromise methanogenesis and (or) augment the biology and biochemistry underpinning alternative hydrogen utilizing pathways. During the initial stages of the project, we will also examine whether a relationship exists between net feed intake and methane production rate, which if established, might support development of gene marker technologies for accelerated animal improvement.
Outcome (as per Commonwealth Agreement)
• From 2012, the combined effects of reduced parasite control costs and improved productivity from use of well adapted cattle and improvements in animal welfare will increase the gross annual revenue of the Australian beef industry by $43 million p.a.
The outcome in Program 3 will be address by the following projects.
Project 3.1.1 ~ Genetic improvement of tick resistance
Strategies and Progress
Ticks and other parasites add a significant cost to the northern cattle industry. The usual tools to control parasites are pesticides, vaccines, and genetic improvement. However, parasites become resistant to more and more pesticides and new pesticides take longer to appear from the pharmaceutical industry. A vaccine against tick fever is available and can be improved, but there is still the issue of the tick burden on cattle and the loss of production that large tick burdens cause. Traditionally, Brahman and other indicus cattle have been used to control the tick, but the industry is moving substantially to taurus x indicus composite breeds. All of this means that reducing tick burdens though genetic means is an issue, given the lack of progress for new pesticides and vaccines.
The main aim of the project is to identify enough DNA markers for resistance to ticks so that 50% of the genetic variance can be identified in genetic tests.
Over the past year, the team studied tick resistance in projects associated with CRCII Project 2.1. In 2006/2007 preliminary studies will begin using more than 30,000 DNA markers to identify DNA markers for tick burden, building on the team’s earlier work in this area. The aim will be to identify and then commercialize the first DNA markers for tick burden in beef cattle.
Project 3.1.2 ~ Novel solutions to improve tick resistance in cattle
Strategies and Progress
Goals of this project include:
• Understand the underlying host mechanisms required for tick resistance, both at the genetic and immunological level
• Understand the breed specific differences which result in tick resistance and tick susceptibility
• Establish laboratory models to identify the molecular and cellular interactions between the tick and host cells
• Develop an immunogenic vaccine based on an annual booster vaccination to protect cattle against ticks
• Develop fast and reliable molecular assays for the detection of acaricide resistance in ticks.
The control of cattle ticks is vital to the continued success of the northern beef cattle industry in terms of compliance with regulatory protocols for intrastate, interstate and international livestock movement, and to enhance animal welfare through avoiding stress and debilitation. The cattle industry in northern Australia incurs ~$175 million in annual losses due to the impact of ticks. The Queensland government spends $3.3 million pa to maintain the tick line between tick endemic and tick free areas, with a large proportion of the State’s export cattle originating from tick endemic areas.
The cattle tick, Boophilus microplus, also transmits babesiosis and anaplasmosis and this tick-disease complex is the most
Program �. Adaptation and Cattle Welfare
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important affecting world-wide livestock production leading to annual global economic losses estimated at >$US2.5 billion due to losses in milk and beef production. Cattle are particularly vulnerable when they first encounter ticks but develop a degree of resistance after repeated exposure. Bos indicus cattle and their crosses (tropical breeds that predominate in northern Australia) develop stronger resistance than do British and European breeds. Modern immunological or genetic techniques have not yet been applied to study this difference in tick susceptibility between cattle breeds.
Chemical treatments (acaricides) are used to control ticks, however ticks have developed resistance to most current acaricides and the current larval packet assay is time consuming and inadequate. Before new tick resistant breeds are available to the cattle industry, the implementation of fast and effective molecular acaricide tests will provide producers with an effective tool for the selection of appropriate acaricide treatment.
The current TickGARD®PLUS tick vaccine is not effective against all stages of the tick and is poorly immunogenic, requiring three or four booster shots per year. The concept of a tick vaccine with 12 month duration of immunity and 90% efficacy is a top priority and was rated highly in a recent MLA survey.
New tick sequence information, in collaboration with the US Department of Agriculture’s B. microplus genome project, will enable the use of a computer (reverse vaccinology) approach for the identification of vaccine candidates. Thus the genome sequence revolution will enable the combining of host immunogenetics with tick sequence data to develop a protective immunogenic tick vaccine.
National and international expertise from the Qld Department of Primary Industries and Fisheries, the University of Queensland, CSIRO Livestock Industries, Murdoch University and the USDA are contributing to this project.
Host response to ticks
The animal sampling component of the first cattle trial has been completed. This trial compares the tick resistance mechanisms of Bos indicus and Bos taurus cattle using immunological assays
and microarrays. There was a larger difference in tick counts between the 2 breeds thus providing an excellent opportunity for studying the underlying divergent immune responses. Our immunological assays have yielded very interesting results in immune cell function in the two cattle breeds.
Tick vaccine
The project team secured further funding ($1.4m) through the Qld Government’s Innovation Project Fund to allow formal collaboration with the USDA, who will provide tick genome data for this research. The funding will also provide resources for ‘proof of concept’ vaccine trials later in the life of the CRC.
A project PhD student has collated published and unpublished tick sequence data and developed computer tools to study tick gene function by comparing Boophilus microplus sequences to other insect and tick species genomes. The research team has also established links with the US-based Ixodes scapularis tick genome project.
The project also collected ticks at different stages of the tick life cycle, to enable the isolation of specific sequences involved in tick attachment and tick survival to further study as potential tick vaccine candidates.
It was recently estimated that the total potential benefit to Australia from the adoption of a new tick vaccine within 5-10years is $32m and within 10-15years is $66m annually. The potential international market of a new tick vaccine is estimated at $US100-185m annually.
Molecular acaricide tests
Preliminary studies have revealed that the same gene mutations responsible for acaricide resistance in ticks in the USA are not present in Australian ticks. Sequence analysis is underway to confirm mutations in Australian tick populations which will provide the basis for the development of rapid molecular assays (24hrs) aimed at replacing the current larval packet testing regime (up to 6 weeks).
Project 3.1.3 ~ Improvement in cattle welfare
The main aims of the project are:
• To develop robust, scientifically defensible measures and critical thresholds that define the welfare status of cattle when exposed to conditions that elicit a sustained stress response when fear is induced or deprived of rest.
• To develop gene marker tests for polled, African horn and scurs genes in Bos indicus and Sanga- derived breeds
Strategies and Progress
Consumer concern for the welfare of animals that produce food and fibre is having increasing impacts on buying behaviour. Further, there is the very real possibility that animal welfare will be used as a market access barrier. The Australian beef industry must be able to assure consumers and markets that animal welfare standards are high. This has been difficult to do because there is an ongoing debate, even amongst animal welfare scientists, as to what is meant by animal welfare and how it should be assessed. This program aims to assist the resolution of
Tick distribution in Australia
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this issue by integrating different methods of welfare assessment based on the behaviour and physiology of the animal, to develop scientifically-defensible, objective measures of animal welfare. These measures can then be used by the Australian beef industry to defend against animal welfare-associated market access barriers, to provide assurances to the general public, markets and consumers and to address problems in production practices that may be revealed. This approach of developing an integrated framework is fully supported by industry (MLA, AWI and Meat and Wool NZ) and national and international animal welfare scientists as evidenced in the report of the MLA/AWI Objective Welfare Measures Workshop held in Sydney in June 2005. There is also agreement that CRC research will be an integral part of the Animal Welfare Objective Measures Research Program which will be jointly overseen by MLA, AWI and Meat and Wool NZ.
Dehorning is routinely practiced in beef cattle, as horns are an important cause of bruising, hide damage and other injuries, particularly in yards, feedlots and during transport. Although it is advisable to dehorn at a young age, because of the mustering practices in northern Australia, dehorning is carried out in older calves between 3.5 and 10 months age. Dehorning in older calves is labour intensive, causes more pain to the animal, takes longer to heal and is prone to secondary infection and mortality in rare cases. Alternately, breeding polled cattle is a non-invasive welfare friendly option. The research proposed in this project aims to develop gene marker tests to allow effective introgressing of polledness in tropical beef cattle, so the practice of dehorning can be phased out.
Thus far, no research program has investigated the possibility of utilising QTL for behaviour and welfare traits, beyond the fact that some adaptation traits, such as tick resistance, have both production and welfare implications. This lack of effort reflects uncertainty about the economic value of such QTL coupled with difficulty in defining and recording welfare and behaviour traits. An opportunity exists to map QTL for behaviour (flight time) and welfare (heat tolerance as indicated by rectal temperature) in an existing data set on the existing CBX cattle population. Data will be analysed to identify new QTL and estimate correlated effects of the QTL. Flight time and rectal temperature will be included among the traits not previously analysed. If substantial QTL are identified the potential value of such QTL will be determined in consultation with industry.
Outcome (as per Commonwealth Agreement)
• A comprehensive genetic improvement package that incorporates genomic and other animal breeding technologies for the genetic improvement of female reproductive performance in breeding cattle resulting in an annual improvement of $46.5 million in the gross revenue of the Australian beef industry from 2012.
The outcome in Program 4 will be address by the following projects.
Project 4.1.1 ~ Gene discovery for post partum re-conception and age of puberty
The aim of this project is to identify diagnostic DNA markers for reduced age at puberty and improved post-partum re-conception in lactating females. These DNA diagnostic markers can then be used to select favourable identification of phenotypes associated with in future populations. To accomplish this task, a strategy consisting of genome scans and fine mapping to identify causative genes has been undertaken.
Strategies and Progress
The initial step in identifying DNA diagnostic markers for age at puberty and post partum reconception was to perform a genome scan (a search of the entire bovine genome) using thousands of single nucleotide polymorphisms (SNPs) to locate regions of the genome that contain genes that influence the measured characteristic. This scan requires access to DNA from cows and heifers where reproductive measurements have been collected.
Selection of animals for the genome scan - Female cattle generated in the CRCII were extensively measured for ovarian activity and subsequent calving performance. The females, run at four different locations in Queensland, are from 2 breeds: purebred Brahman (Bos indicus) and Tropical Composites (containing both Bos indicus and Bos taurus genetics). This population comprises 2,115 females (1,007 Brahman and 1,108 Tropical Composites).
Age at puberty was the first reproductive trait to be targeted in this study, as post partum reconception data had not been completely analysed on all cattle. Genetic analyses on age at puberty data revealed large breed differences in age at puberty. Both breeds have very high heritability estimates for the trait (around 50%). However for Brahmans, the number of females exhibiting a corpus luteum (an indication of ovulation) before commencement of their maiden mating (at 27 months of age) was only 46% compared to 74% for Tropical Composites. This difference is likely to be a major reason for the difference in
Program 4. Female Reproductive Performance
Figure 1. Difference between Brahman and Tropical Composite corpus luteum (CL) production prior to mating (27 months of age) and subsequent calving rate. CL production; 46% for Brahmans vs 74% for Tropical Composites
Calving rate; 70% for Brahmans vs 90% for Tropical Composites.
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subsequent calving rate around of 70% for Brahman and 90% for Tropical Composites. Age at puberty therefore appears to be of far greater importance for overall reproductive performance in Brahmans (when calving is at 3 years of age). Priority was thus given to genotyping Brahmans.
The Brahman females were progeny of 56 sires and were managed after weaning in 3 locations. In total, 585 animals were selected for the initial genome scan for age at puberty. These hiefers were chosen from the two largest sire families plus 5 offspring from each sire-location combination. This ensured maximum genetic variation in the experimental population and also allowed environmental and management differences to be included in the statistical analysis.
SNP genotyping - A genome scan was completed on the 585 animals, using a panel of 10,000 SNPs identified through the international cattle genome sequencing effort. Preliminary analysis of these genotypes is now underway to identify significant regions of the genome containing genes contributing to age at puberty in Brahman cattle.
Project 4.1.2 ~ Expression of genes associated with post partum re-conception
Proof of concept to demonstrate production systems that will optimise the expression of genes for female reproductive performance and maximise the profit delivered by these production systems.
The primary aim of this project is to contribute new information on changes in gene expression that are temporally related to the resumption of ovulation after calving. If consistent relationships between gene expression and ovulation are demonstrated in the different experimental models utilised during the course of the project, it can be concluded the relevant genes are essential to ovulation. This understanding will be used to develop genetic and non-genetic strategies to promote the expression of favourable postpartum genes.
The first postpartum gene expression study will be conducted in late-2006. It will use first-calf Brahman heifers made available by industry. Heifers will be slaughtered at different times after calving to recover tissues for gene expression.
The main target tissue for the first gene expression study is the hypothalamic-pituitary region of the brain. This region of the brain produces and releases a key reproductive hormone, gonadotrophin releasing hormone (GnRH), which initiates a cascade of events required for ovulation. The region is also the site where metabolic and other signalling pathways are integrated to regulate the release of GnRH. Hence, a study of gene expression in this region is expected to yield information on key events that result in qualitative and quantitative changes in
GnRH secretion that precede ovulation. Gene expression will be studied by microarray and quantitative real-time RT-PCR.
Research activity to date has focussed on the consolidation of target genes for expression studies. Primers for RT-PCR have been selected and will be used to develop methodologies with non-experimental brain tissue. This tissue will also be used for preliminary assessment of the oligo microarray slides chosen as the CRC’s microarray platform. The first major experimental data sets from the project will become available in December 2006.
Project 4.1.3a ~ Male indicator traits to improve female reproductive performance
Better predictors of bull fertility to improve reproductive performance of their male and female progeny identified, validated and commercialised by 2012.
The project aims to identify traits in the male that are indicators of female reproductive performance. In doing so, the study will focus on exploring early life predictors of bull fertility both at
Figure 2. Genotyping image indicating the genotypes of one SNP across the 585 Brahman animals.
Research Assistant, Eliza Collis, in front of the ABI3730xl sequencer
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the phenotypic level (his calf output) and at the genetic level (the fertility of his female and male progeny). Except for scrotal size, there is little information on the degree of genetic variation in male reproductive traits and their association with female fertility. Traits such as sperm morphology have been related to calf output in multiple-sire matings in extensive herds. However there is a lack of information on the heritabilities of and genetic correlations between male and female traits. If this project can identify by 12 months of age, bulls that produce more fertile daughters, then the identification of gene markers could be explored to commercialise these results. Early life predictors of fertility in the male will greatly improve the efficiency of selection of sires for improving reproductive performance of beef herds.
Weaner bulls produced from the project will be transferred to either Brigalow Research Station or retained on Belmont Research Station and studied until 24 months of age. Liveweight and scrotal circumference will be measured at 3 monthly intervals with bull breeding soundness examinations (BBSE) conducted at 12, 18 and 24 months of age. The BBSE will involve a physical assessment and collection of semen for morphology examination. About 3500 bulls will be examined from weaning to 2 years of age in 6 cohorts from the CRC herds studying lifetime reproductive performance. The study commenced in April 2005 and will be completed in November 2011.
Field collection of data from the first cohort was completed by November 2005 with laboratory assessment of semen for morphology and concentration completed by February 2006. Semen could be collected from more Composite CCD (C) bulls than Brahman (B) B bulls at 18 months (92% v 47%) but by 24 months, semen could be collected from at least 90% of both B and C bulls (Figure 1). Mean percent normal sperm values were higher in C than in B bulls at both 18 months (66% v 54%) and at 24 months (76% v 69%) (Figure 2).
The second cohort of weaner bulls was weaned in May 2005. A BBSE was conducted over the November 04 – January 05 period (12-14 months of age). Seminal fluid could be collected from 57- 97 % of bulls and semen from 8- 60% of bulls. Mean percent normal sperm was higher in C than B bulls with between 21% and 39 % of C bulls having > 50% normal sperm in an ejaculate compared with 0% in B bulls (Table 1).
At each BBSE, bulls are bled for 11ß hydroxysteroid dehydrogenase, an enzyme involved in cortisol synthesis. Levels of this may explain some of the observed variation in percent normal sperm of bulls. Seminal plasma and semen is being frozen “raw” for detection of “fertility-associated” proteins and for protein polymorphisms as a possible proteomic approach to identify indications of male fertility.
The third cohort of weaner bulls were weaned in May- June 2006.
Project 4.1.3b ~ Early predictors of lifetime female reproductive performance
Early life indicators of female and male reproductive performance identified by 2011.
The broader objective of this project is to identify early life indicators of lifetime female reproductive performance. Currently, an experimental population of 1992 cows is being run at five different locations across Queensland to study their lifetime reproductive performance. This project is using the CRCII cattle resources provided by the Northern Pastoral Group of Companies. Breeding and calving records are being collected at all the research stations adhering to agreed protocols.
Currently there is a lack of data on the genetics of lifetime reproductive performance in female beef cattle and the relationship of this trait with other production traits. Although reproductive rate is perceived to be a lowly heritable trait, there are various underlying component traits affecting overall reproductive performance that could be moderately to highly heritable. The challenge is to identify these traits and include them in selection programs. To identify and quantify the effect of such indicator traits on female lifetime reproductive performance, comprehensive phenotypic measurements of component traits and lifetime fertility are needed in a pedigreed resource population. Such a study will also pave the way for identification of genes affecting lifetime female reproductive performance of beef cattle that would have large economic effects on the productivity of beef cattle enterprises. If these early life indicator traits with strong genetic relationships to lifetime reproductive performance are identified, strategies could be developed to manipulate or alter them to increase the productivity and profitability of the Australian beef herd.
Recently published results from the CRCII analyses of heifer pubertal traits and their associations with female reproductive performance indicate moderate to high heritability estimates of age at presence of first corpus luteum (CL) in Brahmans (0.57) and Tropical Composites (0.52). Other pubertal traits such as days to calving, calving success, ultrasound scanned fat depth at first CL and heifer live weight at first CL are also moderately heritable.
Figure 1. Percentage of No. 4 Brahman and Composite bullslocated at Belmont or Brigalow Research Stations that could be
semen collected
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18 m 24 mAge (months)
% Belmont Brahman
Belmont Composite
Brigalow Brahman
Brigalow Composite
Location Breed Bullsn
Bullsgiving
seminalfluid%
Bullsgivingsemen
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Meannormalsperm
%
Bulls with >50%
normalsperm
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Maximumpercentnormalsperm
%Belmont Brahman 100 57 8 9 0 23
Composite 103 91 55 39 21 95
Brigalow Brahman 127 69 8 19 0 40Composite 242 97 61 57 39 96
Table 1. Seminal traits of Brahman and Composite bulls at 14 months of age
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Genetic correlation estimates indicated that for Brahmans, age at first CL can be used as an indirect selection criterion to improve calving success and days to calving, providing it can be measured cost effectively. Preliminary results from genetic analyses reveal low to moderate heritabilities for adaptive traits: tick scores (0.14 to 0.18), faecal egg counts (0.14 to 0.33), buffalo fly lesion scores (0.17), rectal temperatures (0.13 to 0.26), coat scores (0.15 to 0.50), and coat colour (0.54). Further recording of data would enable us to estimate the genetic correlations between lifetime reproductive performance attributes and the adaptive traits in tropical breeds. This is essential to answer questions such as whether the use of advanced genetic marker technologies to improve carcass and meat quality and reproductive performance have any adverse effect on adaptability of the animals to tropical conditions.
The role of the Underpinning Science Program is to coordinate the CRC activities that span more than one subprogram and in particular to provide technology platforms that can be used throughout the CRC.
Strategies and Progress
The Underpinning Science program has a number of goals, including to:
• maintain databases of CRC information.
• maintain a collection of DNA from CRC animals
• coordinate genotyping and microarrays across the research programs
• coordinate analysis of genotype and microarray data across research programs
• provide bioinformatic support that is CRC specific or that cannot otherwise be obtained by members of the CRC
The four scientific programs of the CRC have a common need for access to technology and support in certain areas such as the maintenance of databases and data analysis. The Underpinning Science program provides this support and coordinates activities, that more than one program might use.
Databases - These databases are a major asset of the CRC. A secure, web-accessible database of phenotypic data and pedigrees maintained in CRC I and II is being continued and CRC III data are being added. In addition, genotype and microarray data are directly linked to this phenotypic database.
DNA - As for the databases, the DNA from CRC animals represents a major asset of the CRC and will be used for on-going research. DNA from CRC I and II cattle is currently stored at CSIRO. A part of the collection has been duplicated and stored at DPI Victoria to provide greater security. An audit of all CRC materials is currently underway in order to decide how best to maintain them for future use.
Genotyping, microarrays and major animal experiments - Genotyping, microarrays and large cattle experiments are costly activities and are used by all four research programs. The project works with the Underpinning Science Committee to coordinate these activities. One of its activities has been to agree on a common platform for microarray experiments across the CRC.
Analysis of QTL mapping and microarray experiments - Analysis and interpretation of data will primarily be the responsibility of the scientists undertaking the experiments. However the statistical analysis of whole genome and microarray data is not straightforward and expertise in this area is scarce. Therefore the Underpinning sciences program will employ three scientists to service the needs of all programs to assist in experimental design and data analysis, especially genotype and microarray data.
Bioinformatics support - Most organisations involved in the CRC have their own bioinformatics service and these can be built into individual projects. However, there is a common need for access to information based on the bovine genome sequence. CSIRO is therefore providing the CRC with access to its bovine genome resources.
Figure 2. Mean percent normal sperm in ejaculates of No. 04 Brahman andComposite bulls at Belmont and Brigalow Research Stations
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45
50
55
60
65
70
75
80
18mo 24mo
Age (months)
%
04 Belmont Brahmans
04 Belmont Composites
04 Brigalow Brahmans
04 Brigalow Composites
Program 7. Underpinning Science
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Research Collaboration
Collaborative elements of the Beef CRC’s research programs are illustrated in the diagrams below. The CRC’s programs and projects cut across both site (see map below) and institutional barriers, with linkages within and across programs. There are no serious constraints imposed by institutional boundaries. The Underpinning Science Program is linked to all the research programs and provides across-program linkage in the coordination of research and sharing of genomics resources. The Education and Training Program is also linked to all research programs and serves a similar role across programs in the provision of education, awareness and accelerated adoption services. Each of the projects undertaken in 2005/06 involved work done at several locations and with staff from at least three participant organisations.
The Beef CRC program activities include involvement of over 40 industry partners as either core and supporting industry participants or sponsors (listed earlier under “Industry Sponsors”). These industry collaborators are key partners in the development and implementation the CRC’s research, education and adoption strategies. For example, the CRC’s research projects also include industry breeding cows which generate experimental progeny to underpin research activities in the programs. It is a feature of the CRC’s Program that effective, cooperative research can be carried out in close harmony with private sector cattle business.
The Beef CRC has collaborative agreements with the Sheep CRC in undertaking the web-based Livestock Library project and also through joint post-graduate education activities. Informal collaborative arrangements exist between the Beef CRC and the Sheep Genomics Project and the Dairy CRC.
RESEARCH COLLABORATION
NationalNetwork Sites
Rockhampton, QldBrisbane, Qld
Glen Innes, NSWArmidale, NSWMelbourne, Vic
Adelaide, SAPerth, WAVasse, WA
End-UserLinkages
ABRIBeef Improvement Assoc
John Dee Warwick P/LAustralian Country Choice
Rockdale Beef P/L
NationalNetwork Sites
Trangie, NSWStruan, SAVasse, WA
Melbourne, VicCamden, NSWAdelaide, SA
Armidale, NSWHamilton, VicBrisbane, Qld
End-UserLinkagesAngus Society
ABRIBeef Improvement Assoc
NationalNetwork Sites
Rockhampton, QldBrisbane, Qld
Armidale, NSW
End-UserLinkages
ABRINational AnimalWelfare StrategyWorking Groups
NationalNetwork Sites
Rockhampton, QldBrisbane, QldMillaroo, QldGayndah, Qld
Julia Creek, QldTheodore, QldArmidale, NSW
End-UserLinkagesAgForce Qld
Northern Pastoral GroupABRI
Australian BrahmanBreeders Association
High Quality Beef
Feed Efficiencyand Responsible
Resource Use
Adaptation andCattle Welfare
FemaleReproduction
InternationalNetwork Sites
KoreaIrelandFrance
New Zealand
InternationalNetwork Sites
USA
InternationalNetwork Sites
InternationalNetwork Sites
USANew Zealand
USA
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International Collaboration
There were 15 international collaborations that were active in 2005/06. The Beef CRC has formal collaborative arrangements with Meat and Wool New Zealand as a core participant, and has entered into an agreement with Ohio State University (OSU), as a Supporting Participant. OSU brings into the CRC world-leading research capability in the area of rumen microbial genomics plus expertise and resources in IGF–I genotypes to enhance the research in Programs 2 and 4. A materials transfer agreement was signed this year between USDA and QDPI&F and Murdoch University to transfer USDA’s unpublished cattle tick expressed sequence tag (EST) data for use in CRC Program 3.
In addition, there were informal collaborative arrangements with several international institutions and organisations, including the National Livestock Research Institute (NLRI) of South Korea, that were active during 2005/06. Negotiations with NLRI to formally become a Supporting Participant are at an advanced stage. NLRI brings to the CRC expertise and capacity in meat science and animal genomics. The other organisations are in France, Ireland, Japan, South Africa and the United States, with discussions currently underway to formalise these arrangements.
The CRC also collaborated with EMBRAPA in Brazil and the International Livestock Reserach Institute (ILRI) in Kenya to develop new genotyping tools for use in Bos indicus cattle.
Rockhampton
Brisbane
Armidale (Beef CRC HQ)
Melbourne
AdelaidePerth
Wellington
Beef CRC Major Research Sites
Research StationsBelmont, Qld
Brian Pastures, QldBrigalow, Qld
Swans Lagoon, QldToorak, Qld
Glen Innes, NSWTrangie, NSW
Tullimba, NSWHamilton, Vic
Struan, SAVasse, WA
National Network
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Education and Training > Postgraduate Education
> Undergraduate Education
> Awareness Activities
> Accelerated Adoption
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Education and Training
The main aim of this program is to produce a skilled beef industry workforce resulting from postgraduate, undergraduate and vocational training in the sciences underpinning beef genetic improvement and effective innovation, commercialisation and adoption of outcomes by the beef industry.
Project 5.1. Postgraduate Education
Strategies and Progress
There is a shortfall of tertiary trained students with technical and research skills in both the traditional basic sciences and the science of effective innovation and adoption in all sectors of the beef industry. To address this shortfall, the CRC aims to support at least 35 postgraduate students to undertake higher degree training in the sciences that underpin programs 1 to 5 over the life of the CRC. CRC scholarships will be offered at PhD and Masters level to Australian and overseas students associated with our international partner organisations.
As part of the first intake of postgraduate students, scholarships were advertised in October 2005. Twelve applications were
received and although there were only 7 scholarships budgeted, the quality of students was exceptionally high and it was agreed the opportunity would be lost if such good quality students were rejected. Hence the budgets were reworked and by staggering the starting dates and embedding some scholarships within projects it was possible to offer a total of 11 scholarships to commence by July 2006. Hence the CRC is well on track to meet its target of at least 35 postgraduate students. The supervisors of the students are from university and/or other non-university participant organisations. While there are no current students with direct industry supervisors, the research of four postgraduate students has direct industry involvement. The project also oversaw Beef CRC II postgraduate students finishing their degrees. Upon completion of their degrees most of the students gained employment, with responsibilities related to animal science, hence contributing to skills development in agriculture. The table below summarises the destination of students who completed their degrees or were in the final stages during 2005/06.
Graduate Employment Destination for CRCII students
Name Institute Completion Graduate Employment DestinationCRCII - Receiving funding in 2005/06Kelly Drake UNE Writing up Postdoctoral position at Oxford UniversityCedric Gondro UNE Submitted Post Doc at UNEBrad Walmsley UNE Writing up Looking for Post Doc overseasLysandra Slocombe UNE Writing up Looking for a Post DocFiona Jones Murdoch University Writing upScott Foster Adelaide University Submitted Research Scientist with TIAR (Ag Tasmania)
CRCII - Students Graduating in 2005/06Briana Daly UNE PhD awarded Lecturer animal science UNEAndrew Alford UNE PhD awarded Research Officer with NSW DPIBen Wood UNE PhD awarded Geneticist - Turkey breeding company - based in
CanadaSiok Hwee Tan UNE PhD awarded Post Doc at IMB UQDavid Beatty Murdoch University PhD awarded Lecturer in physiology at Murdoch Vet SchoolGareth Kelly UNE MSc awarded Trainee Priest at WalchaAlvaro Simeone UNE PhD awarded University of Uruguay (teaching and research) Michael Beer UNE MSc awarded Livestock Officer NSW DPI - TamworthMalcolm McPhee UC-Davies, USA PhD awarded Research Scientist, NSW DPI - ArmidaleChristopher White Melbourne University MSc awarded Completed Dip Ed - Teaching at High School in Victoria
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Project 5.1.2 ~ Undergraduate Education
Strategies and Progress
This project provides support for the development of undergraduate and vocational training courses and workshops to be delivered to the Australian and New Zealand beef industries. Courses will be delivered through a variety of
providers including Universities, industry training organisations, TAFEs, Agricultural Colleges and secondary schools. In addition this program provides summer scholarships to undergraduate students as a mechanism of encouraging them to undertake postgraduate studies within the Australian beef industry.
Summer scholarships were offered to 9 undergraduate students, comprising 3 at the University of New England, 2 at Murdoch
2005/2006 Beef CRCIII Postgraduate Students
Student Course Thesis Topic University Supervisor(s0 Funding StatusHeidi Rodgers PhD The economics of
quality differentials in beef
University of New England
Garry GriffithEuan Fleming
Beef CRC In progress
Hayley Moreland PhD Facilitating uptake of productivity enhancing technologies within beef supply chains – an action research approach
University of Queensland
Don Cameron Beef CRC In progress
Ainu Husna M S Suhaimi
PhD Post-partum anoestrus in cows: gene expression profiling of the preoptic area and hypothalamus
University of Quensland
Sigrid LenhertMichael D’Occhio
Beef CRC + MARDI (Malaysia)
In progress
Dannielle Hulett PhD Identification of DNA markers associated with beef cattle feed efficiency
University of Melbourne
Mike GoddardBrian LeuryHelen McPartlinBen HayesBrendan Tathum
Beef CRC + University of Melbourne
In progress
Michael Laurence PhD Maternal productivity investigations in beef cattle
Murdoch University
Anne BarnesDave PethickJeisane Accioly
Beef CRC In progress
Sebastian Kurscheid
PhD Identification of novel tick therapeutic targets
Murdoch University
Matt BellgardAla Lew
Beef CRC In progress
Emily Piper PhD Changes in immune responses and gene expression of tick resistant versus susceptible cattle
University of Queensland
Nicholas JonnsonLouise Jackson
Beef CRC In progress
Andrew Egarr PhD The molecular genetics of fat deposition in cattle
University of Adelaide
Cynthia BottemaWayne Pitchford
University of Adelaide and Beef CRC top-up
In progress
Kirsty Moore PhD Using DNA technologies in Australian beef cattle breeding
University of New England
David JohnstonJohn Gibson
MLA In progress
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University, 2 at Queensland University and 1 each at Melbourne and Adelaide Universities.
This project included a half time position for the Project Manager. To supplement this MLA, has agreed to provide the other half of the salary to allow a full time position to be advertised. The MLA component of the position will provide support for the processing and grading areas within MLA. In return for the MLA part-time position UNE has confirmed that it will replace the current professorial Meat Science position at UNE when it becomes vacant in 2009.
The Project Manager position was advertised in February 2006 and a number of applicants were interviewed in April 2006. Dr Geert Geesink from the CCL Research group in the Netherlands has accepted the position and is currently organising a visa to commence duties in late 2006.
This project provided support for several CRC events, including the beef industry Feeder Steer School held in Armidale in February 2006 which was attended by 82 delegates.
Support was also given to a CRC visit to NZ to present a series of 10 workshops in the north and south islands. The workshops were conducted in association with the Beef Council, Meat and Wool New Zealand and breed associations and were attended by 892 participants with representation from farm consultants, the stock and station industry, dairy, sheep and beef industries and veterinarians.
Project 5.2.1 ~ Awareness
The Beef CRC has produced a wide variety of outcomes for adoption. There is a need to ensure that outcomes from the CRC are packaged in a manner that will facilitate implementation. In addition to the accelerated adoption activities there is still a need for producers to be made aware of the outcomes.
Livestock Library
A large volume of animal production research and extension papers has been published over the past 50 years. Whilst this information is still highly relevant to today’s livestock industries, it is often difficult to access. On-line access to this information will assist producers, technology transfer specialists, students or researchers to gain additional skills and knowledge and to make more informed decisions. The Livestock Library is a collaborative project with the Sheep CRC to provide an electronic library with ‘free to air’ access for a range of users. The library provides access to previously published scientific, technical and extension articles which are relevant to the Australian and New Zealand Livestock industries. It was publicly launched at the Association for the Advancement of Animal Breeding and Genetics conference in September 2005.
Prior to the launch there were about 200 registered users of the Livestock Library. By the end of September 2005 there were about 600 registered users. Since then there has been a steady increase in the number of users registering, as shown in Table 1. Usage of the Livestock Library continued to increase over 2005/2006.
A part time Manager for the Livestock Library was appointed in February 2006. Since then enhancements have been undertaken to both the Livestock Library website and the
Table 1. Livetock Library User Registrations
Date New Registered Users This
Month
Cumulative Total of Registered
Users
Prior to 31.08.05 197Sept 05 54 251Oct 05 195 446Nov 05 246 692Dec 05 163 855Jan 06 131 986Feb 06 123 1,109Mar 06 204 1,313
Beef CRC Website
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management of information on the site to make it more user-friendly and intuitive. A project to improve information retrieval of documents in the Livestock Library, was also initiated. Written copyright clearances are being sought for the conference proceedings that are hosted on the site including those from the Association for the Advancement of Animal Breeding and Genetics Proceedings, Australian Society of Animal Production Proceedings and Recent Advances in Animal Nutrition.
Beef CRC Web Site
The web is an important communication tool for on-going activities and programs in the Beef CRC. Clients who access the CRC website include staff, industry stakeholders and beef industry businesses. A pre-requisite for a successful web site is that the information can be easily interpreted by all end-users, ranging from scientists to producers. The Beef CRC web site also acts as a point of entry (along with other sites from core and supporting parties) to the Livestock Library.
Project 5.2.2 ~ Accelerated Adoption through “Beef Profit Partnerships”
The Beef CRC has established Beef Profit Partnership (BPP) teams to accelerate the adoption of technology in the Australian beef industry. The teams are using the principles of accelerated adoption as part of a cycle involving measurement, monitoring and evaluation. The progress of the BPP groups is being documented as part of a Beef CRC monitoring program will underpin the achievement of CRC commercialisation outputs and profitability outcomes in industry.
Progress and Strategies
The Accelerating Adoption through Beef Profit Partnerships project is an integral part of the CRC’s strategy for education, training, awareness and adoption, as shown in Figure 1.
Figure 1 The Beef CRC education, training, awareness and adoption strategy.
It involves development of an adoption system focused on achieving measurable outcomes across a network of Beef Profit Partnership teams (BPPs). The measured outcomes of BPPs underpin the achievement of commercialisation outcomes of the Beef CRC.
The BPPs are conducted using the principles of Continuous Improvement and Innovation, involving an ongoing cycle of focus, action, measurement and evaluation. This involves setting Key Performance Indicators and performance targets and then using the beef industry profitability framework to assess the potential impact of new technology. This process of measurement, monitoring and evaluation is undertaken at regular intervals and progress monitored using cost of production calculators and gross margin tools. BPPs meet at scheduled intervals for action tracking and support (0, 90, 180 & 270 days). The teams determine their own adoption focus, objectives and activities. The Profit Driver Framework, shown in Figure 2 is used to
monitor and evaluate profitability outcomes.
Fifty Beef Profit Partnership teams were initiated or are planned across Australia and New Zealand. They include supply chain groups (with Program 1) and regional producer groups. The breakdown of the teams across regions are:
• QLD 18 producer BPPs, 2 supply chain partnerships
• NSW 12 producer BPPs, 2 supply chain partnerships
• Vic 6 producer BPPs
• SA 3 producer BPP
• WA 3 producer BPPs, 1 supply chain partnership
• New Zealand 3 producer BPPs
Capacity building workshops and activities were conducted to equip the BPPs with methods and technologies required for continuous improvement that BPPs have close linkages to CRC Awareness activities and other extension/training opportunities by the participant organisations and MLA.
Figure 2. Profit driver framework, to be used to monitor and evaluate profitability outcomes in CRC Beef Profit Partnerships
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Outcome
The Beef CRC is entering a new phase for communication. Currently in its first year the new Beef CRC needs to establish an identity and brand for the new centre.
Implementation of a communication plan for the Beef CRC will allow the communications team and the centre to set aims and goals to accomplish effective two-way communication, establish a strong corporate culture and reputation and ensure ongoing commitment and support by all stakeholders
The ultimate goal of the communication project as a whole is to increase awareness and knowledge of the Beef CRC, while also firming the Centre’s reputation as Australia’s leading source of world class beef science and technology.
The communication plan provides objectives, strategies, implementation and evaluation methods to ensure outcomes foster and improve collaboration, deliver knowledge and build and maintain company activities with the CRC’s key stakeholders, as well as promoting and encouraging the sharing of information between CRC staff across Australia and internationally.
The communication plan provides a framework to deliver and aid the adoption of key messages and results of world class gene discovery and gene expression research to improve profitability, productivity and animal welfare for external and internal stakeholders and Australia’s beef industry as a whole.
Key Objectives and Target Audience
The Beef CRC brings together the interests of a range of stakeholder groups, both external and internal, both international and domestic. Stakeholders include staff, government, industry and research funders/providers. To ensure the differing nature and requirements of each group are achieved, four key target audiences have been identified each with its own key objective.
Strategies and Progress
To ensure the target audiences and their key objectives are achieved a range of strategies have been identified to deliver key messages and information.
The needs of each target audience differ and strategy requirements change accordingly. For example the strategies needed to deliver key messages and information to an Industry audience differ to those needed for communication with the Board/Participants/Supporting Participants audience.
The Communication strategy is closely linked with the Awareness and Accelerated Adoption projects in Program 5. Activities in both projects include involvement and linkages with beef industry enterprises ranging from large to small beef business enterprises. In the Accelerated Adoption project, for example, the CRC has formed 50 Beef Business Partnership (BPP) groups to accelerate adoption of CRC and other research outcomes. Most of the BPP groups are made up of 7 or more small business enterprises per group, while 5 BPP groups are made up of supply chain alliances of small-medium and large scale beef businesses. These linkages with the SMEs will help to accelerate the adoption of Beef CRC outcomes.
Communication Strategy and Specified Personnel
AIMIncrease Beef CRC
profile and reputation
Industry
Board
/Participants/SupportingParticipants
St
aff/
Rese
arch
ers
Med
iaTARGET AUDIENCES
Website Internal newsletters
Externalnewsletters
Em
ailupdatesDirectmailoutsPressreleasesAnnualRep
ort
Stak
ehol
der/
Part
icip
ant l
iais
onan
dre
latio
nship
buildingStakeholder / Participant / Governm
ent networking
opportunities
MediaAlertsParticipate/HostIndustryEventsNati
onal
Foru
ms
and
Info
rmat
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Sess
ions
Communication Material
Media relationshipbuildi ng
(toassistinfluenceandmanoeuvrethemedia)Mediacoverag
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Inte
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Briefin
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STRATEGIES
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Specified Personnel Their contributing organisation
Their position in the CRC The percentage of their time contributed to CRC activities
Any changes during the year (Approval required for 2000 agreements only)
Dr Heather Burrow Beef CRC Ltd Chief Executive Officer 100
Dr Paul Arthur NSW Dept of Primary Industries
Deputy Chief Executive Officer 56
Mr Geoff Allen Beef CRC Ltd Finance and Business Development Manager
100
Prof David Pethick Murdoch University Program Manager 38
Dr Wayne Pitchford University of Adelaide Program Manager 60
Prof John Gibson University of New England
Program Manager 28
Mr Jim Walkley Qld Dept of Primary Industries & Fisheries
Program Manager 69
Prof John Thompson University of New England
Program Manager 58
Prof Mike Goddard Vic Dept of Primary Industries
Program Manager 20
Specified Personnel
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Publications > Journal Papers and Book Chapters
> Refereed Conference Proceedings
> Non-refereed Conference Proceedings
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Journal Papers and Book Chapters
Alford, A.R., Hegarty, R.S., Parnell, P.F., Cacho, O.J., Herd, R.M. and Griffith, G.R. (2006), “The impact of reducing residual feed intake on enteric methane emissions from the Australian beef industry”, Australian Journal of Experimental Agriculture, 46 (6-7) pp.813-820.
Ambarawati, I.A., Zhao, X., Griffith, G.R. and Piggott, R.R. (2006), “Bali beef industry: An equilibrium displacement model approach”, Journal on Socio-Economics of Agriculture and Agribusiness, Vol. 6, No. 1 (accepted, in press).
Arthur PF, Herd RM, Wilkins JF and Archer JA (2005) Maternal productivity of Angus cows divergently selected for post-weaning residual feed intake. Australian Journal of Experimental Agriculture 45, 985-994.
Barendse W (2005) The transition from quantitative trait loci to diagnostic test in cattle and other livestock. Australian Journal of Experimental Agriculture 45, 831-836.
Barwick SA and Henzell AL (2005) Development successes and issues for the future in deriving and applying selection indexes for beef breeding. Australian Journal of Experimental Agriculture 45, 923-934.
Beatty, D.T., Barnes, A., Taylor, E. Pethick, D., McCarthy, M. and Maloney, S.K. (2006). The physiological responses of Bos taurus and Bos indicus to prolonged and continuous heat and humidity. Journal of Animal Science 2006, 84:972-985.
Bell, A.W., Greenwood, P.L. and Ehrhardt, R.A. (2005). Regulation of metabolism and growth during prenatal life. In: Biology and Metabolism of Growing Animals, editors D.G. Burrin and H.J. Mersmann, pp. 3-34. Elsevier Science B.V., Amsterdam.
Burrow HM and Bindon BM (2005) Genetics research in the Cooperative Research Centre for Cattle and Beef Quality. Australian Journal of Experimental Agriculture, 45, 941-958.
Burrow HM, Anderson CA and Muir LL (eds., 2006) “The Impact of Science on the Beef Industry”. Australian Journal of Experimental Agriculture Special Edition Volume 46, 144 pages.
Café LM, Hennessy DW, Hearnshaw H, Morris SG and Greenwood PL (2006) Influences of nutrition during pregnancy and lactation on birth weights and growth to weaning of calves sired by Piedmontese or Wagyu bulls. Australian Journal of Experimental Agriculture 46, 245-256.
Colditz IG, Watson DL, Kilgour R, Ferguson DM, Prideaux C, Ruby J, Kirkland PD and Sullivan K (2006) Impact of animal health and welfare research within the CRC for Cattle and Beef Quality on Australian beef production. Australian Journal of Experimental Agriculture 46, 233-244.
Corbet NJ, Shepherd RK, Burrow HM, Prayaga KC, van der Westhuizen J and Strydom PE (2006) Evaluation of Bonsmara and Belmont Red cattle breeds in South Africa. 1. Productive
performance. Australian Journal of Experimental Agriculture 46, 199-212.
Corbet NJ, Shepherd RK, Burrow HM, Prayaga KC, van der Westhuizen J and Bosman DJ (2006) Evaluation of Bonsmara and Belmont Red cattle breeds in South Africa. 2. Genetic parameters for growth and fertility. Australian Journal of Experimental Agriculture 46, 213-224.
Dalrymple BP (2005) Harnessing the bovine genome sequence for the Australian cattle and sheep industries. Australian Journal of Experimental Agriculture 45, 1011-1016.
Drinkwater RD, Li Y, Lenane I, Davis GP, Shorthose R, Harrison BE, Richardson K, Ferguson D, Stevenson R, Renaud J, Loxton I, Hawken RJ, Thomas MB, Newman S, Hetzel DJS and Barendse W (2006) Detecting quantitative trait loci affecting beef tenderness on bovine chromosome 7 near calpastatin and lysyl oxidase. Australian Journal of Experimental Agriculture 46, 159-164.
Entwistle KW, Cummins LJ, Hillard MA, Kinder JE, O’Shea T, Piper LR, Thimonier J and Wilkins JF (2006) Bernard Michael Bindon – reproductive physiologist, animal scientist, research leader. Australian Journal of Experimental Agriculture 46, Foreword pp. i – xii.
Goddard ME and Meuwissen THE (2005) The use of linkage disequilibrium to map quantitative trait loci. Australian Journal of Experimental Agriculture 45, 837-846.
Graser H-U, Tier B, Johnston DJ and Barwick SA (2005) Genetic evaluation for the beef industry in Australia. Australian Journal of Experimental Agriculture 45, 913-922.
Greenwood PL, Café LM, Hearnshaw H, Hennessy DW, Thompson JM and Morris SG (2006) Long-term consequences of birth weight and growth to weaning on carcass, yield and beef quality characteristics of Piedmontese- and Wagyu-sired cattle. Australian Journal of Experimental Agriculture 46, 257-270.
Greenwood, P.L., Gardner, G.G. and Hegarty R.S. (2006). Indices of cellular development in muscles of lambs are influenced by sire estimated breeding values and pastoral nutritional system. Australian Journal of Agricultural Research 57:651-659.
Greenwood, P.L., Davis, J., Gaunt, G.M. and Ferrier, G.R. (2006) Influences on the loin and cellular characteristics of the m. longissimus lumborum of Australian Poll Dorset-sired lambs. Aust J Agric Res 57:1-12
Greenwood, P.L., Gardner, G.G. and Hegarty R.S. (2006) Myofibre characteristics are influenced by sire estimated breeding values and pastoral nutritional system. Australian Journal of Agricultural Research 57:627-639.
Publications
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Griffith, G.R. (2005), “Economic impact of a major beef industry research and development investment: the renewal of the Cooperative Research Centre for Beef Genetic Technologies”, Australian Journal of Experimental Agriculture (accepted subject to revision).
Hammond K (2006) Breeding strategies for the development of the Australian beef industry: an overview. Australian Journal of Experimental Agriculture 46, 183-198.
Harper, G.S., Lehnert, S.A. and Greenwood, P.L. (2005) Nutrition-gene interactions (post-genomics): Changes in gene expression through nutritional manipulations In: Applications of Gene-based Technologies for Improving Animal Production and Health in Developing Countries. Editors H.P.S. Makkar, and G.J Viljoen, pp. 411-428. Springer, The Netherlands, IAEA.
Hwang, I.H., Polkinghorne, R., Lee, J.M., Thompson J.M. (2006) Demographic and design effects on beef sensory scores given by Korean and Australian consumers. Journal of Experimental Agriculture (accepted)
Jeon J-T, Lee J-H, Kim, K-S, Park C-K and Oh S-J (2006) Application of DNA markers in animal industries. Australian Journal of Experimental Agriculture 46, 173-182.
Kadel MJ, Johnston DJ, Burrow HM, Graser H-U, Ferguson DM (2005) Genetics of flight time and other measures of temperament and their value as selection criteria for improving meat quality traits in tropically adapted breeds of cattle. Australian Journal of Agricultural Research, 2006, 57, 1029-1035.
Klieve, A.V. 2005. 2.2. Bacteriophages, p. 39 – 46. In Methods in gut microbial ecology for ruminants. H.P.S. Makkar and C.S McSweeney (ed.) International Atomic Energy Agency. Springer Academic Press.
Klieve, A.V. and R.A. Gilbert. 2005. 4.2 Bacteriophage populations, p. 129 - 137. In Methods in gut microbial ecology for ruminants. H.P.S. Makkar and C.S McSweeney (ed.) International Atomic Energy Agency. Springer Academic Press.
Lehnert SA, Wang YH, Tan SH and Reverter A (2006) Gene expression-based approaches to beef quality research. Australian Journal of Experimental Agriculture 46, 165-172.
Lew AE, Jackson LA and Bellgard MI (2005) Comparative genomic analysis of non-coding sequences and the application of RNA interference tools for bovine functional genomics. Australian Journal of Experimental Agriculture 45, 995-1010.
McKiernan WA, Wilkins JF, Barwick SA, Tudor GD, McIntyre BL, Graham JF, Deland MPB and Davies L (2005) CRC “Regional Combinations” project – effects of genetics and growth paths on beef production and meat quality: experimental design, methods and measurements. Australian Journal of Experimental Agriculture 45, 959-970.
Morrison, M., Adams, S.E., Nelson, K.E. and Attwood, G.T. (2005) Metagenomic analysis of the
microbiomes in ruminants and other herbivores. pp. 209-220. In: Methods in Gut Microbial Ecology (Makkar, H.P., and McSweeney, C.S., Editors) Springer Science, Dordrecht.
Nengovhela NB, Matjuda LE, Motiang DM, Madzivhandila TP, Banga C, Masia S and Clark RA (2006) Achieving sustained improvements in profitability in the emerging sector of the South African beef industry. ACIAR Special Issue of Australian Journal of Experimental Agriculture (submitted).
Nicholas FW (2006) Discovery, validation and delivery of DNA markers. Australian Journal of Experimental Agriculture 46, 155-158.
O’Rourke B.A., Dennis J.A. and Healy P.J. (2006). Internal restriction sites: quality assurance aids in genotyping. J Vet Diag Invest 18:195-197.
O’Toole, D., Montgomery, D. L., Steadman, L., O’Rourke, B., Russell, W. and Dennis. J. (2005). Status spongiosis in newborn Gelbvieh calves. J Vet Diag Invest 17:546-553
Perry, D and Thompson, J.M. (2005) The effect of growth rate during backgrounding and finishing on meat quality traits in beef cattle. Meat Science 69 691-702
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Pethick, D.W., Fergusson, D.M., Gardner, G.E., Hocquette, J.F., Thompson, J.M. and Warner, R. (2005) Muscle metabolism in relation to genotypic and environmental influences on consumer defined quality of red meat . In Indicators of milk and beef quality. Eds J.F.Hocquette and S.Gigli. EAAP publication No.112. pp. 95-110. Wageningen Academic Publishers.
Pethick, D.W. Harper, G. and Dunshea, F.D. (2005) Fat metabolism and turnover. In Quantitative aspects of ruminant digestion and metabolism. Pp345-372. Eds. J. Dijkstra, J.M. Forbes and J. France. CABI Publishing, Wallingford, UK.
Pitchford WA, Mirzaei HM, Deland MPB, Afolayan RA, Rutley DL and Verbyla AP (2006) Variance components for birth and carcass traits of crossbred cattle. Australian Journal of Experimental Agriculture 46, 225-232.
Prayaga KC and Henshall JM (2005) Adaptability in tropical beef cattle: genetic parameters of growth, adaptive and temperament traits in a crossbred population. Australian Journal of Experimental Agriculture 45, 971-984.
Prayaga KC, Reverter A, Burrow HM, Anderson CA and Muir LL (eds., 2005) “Application of New Genetic Technologies to Animal Breeding”. Australian Journal of Experimental Agriculture Special Issue, 45 (7-8), 305 pages.
Reverter A, Barris W, Moreno-Sanchez N, McWilliam S, Wang YH, Harper GS, Lehnert SA and Dalrymple BP (2005) Construction of gene interaction and regulatory networks in bovine skeletal muscle from expression data. Australian Journal of Experimental Agriculture 45, 821-830.
Schutt KM, Burrow HM, Thompson JM and Bindon BM (2006) Carcass quality of Brahman and first-cross cattle grown on pasture and grain in subtropical and temperate Australia. Australian Journal of Agricultural Research (submitted).
Schutt KM, Burrow HM, Thompson JM and Bindon BM (2006) Meat quality and palatability of Brahman and first-cross cattle grown on pasture and grain in subtropical and temperate Australia. Australian Journal of Agricultural Research (submitted).
Tan SH, Reverter A, Wang YH, Byrne KA, McWilliam SM and Lehnert SA (2006) Gene expression profiling of bovine in vitro adipogenesis using a cDNA microarray. Functional and Integrative Genomics 10:1-15
Thompson, J.M., Polkinghorne, R., Hwang, I.H., Gee, A.M., Cho, S.H., Park B.Y., and Lee J.M. (2006). Beef quality grades as determined by Korean and Australian consumers. Australian Journal of Experimental Agriculture (accepted)
Vere, D.T. and Griffith, G.R. (2005), “The benefits of integrating econometric models for economic analysis in the Australian livestock industries”, The Empirical Economics Letters 4(3), 145-156.
Wang YH, Reverter A, Mannen H, Taniguchi M, Harper GS, Oyama K, Byrne KA, Oka A, Tsuji S and Lehnert SA (2005) Transcriptional profiling of muscle tissue in growing Japanese Black cattle to identify genes involved with the development of intramuscular fat. Australian Journal of Experimental Agriculture 45, 809-820.
Whan I, Bortolussi G and Backus R (2006) The impact of innovation
on beef production in far northern Australia. Australian Journal of Experimental Agriculture 46, 271-282.
Womack JE (2006) The impact of sequencing the bovine genome. Australian Journal of Experimental Agriculture 46, 151-154.
Refereed conference proceedings
Cafe, L.M, Hearnshaw, H., Hennessy, D.W. and Greenwood, P.L. (2006). Growth and carcass characteristics of Wagyu-sired steers at heavy market weights following slow or rapid growth to weaning. Aust J Exp Agric (in revision for ASAP Edition)
Deland MPB, Siebert B, Graham JF and Hebart M (2005) Sire selection for yield or intramuscular fat and beef quality. Proceedings Association for the Advancement of Animal Breeding and Genetics 16, 381-384.
Farrell RA, Edmondston VJ, Bertram JD, Venamore P and Hudson S (2005) Delivering new CRC technologies to the northern beef industry. Proceedings Association for the Advancement of Animal Breeding and Genetics 16, 405-408.
Gardner, G.E., Martin, K.M., McGilchrist, P. and Thompson, J.M. (2005). The impact of selection for muscling on carbohydrate metabolism. Asia Pacific J Clin Nutr 14 (supplement): S26.
Graham JF, Byron J, Deland MPD and Kearney G (2005) Effect of post-weaning growth and bulls selected for extremes in intramuscular fat and retail beef yield on liveweight and carcase traits. Proceedings Association for the Advancement of Animal Breeding and Genetics 16, 338-341.
Greenwood, P.L., Cafe, L.M., Hearnshaw, H. and Hennessy, D.W. (2005). Consequences of growth retardation early in the life of cattle. Proc Nutr Soc Aust Vol. 29. Asia Pacific J Clin Nutr 14 (supplement): S25.
Greenwood, P.L., Cafe, L.M., Hearnshaw, H. and Hennessy, D.W. (2005) Consequences of nutrition and growth retardation early in life for growth and composition of cattle and eating quality of beef. Rec Adv Anim Nutr Aust 15:183-195
Hegarty RS, Herd RM, Goopy JP, McCorkell B and Arthur PF (2005) Selection for residual feed intake can change methane production by feedlot steers. Proceedings Association for the Advancement of Animal Breeding and Genetics 16, 334-337.
Herd RM, Arthur PF and Archer JA (2005) When pastures limit growth rate of steers those bred for low residual feed intake grow faster. Proceedings Association for the Advancement of Animal Breeding and Genetics 16, 330-333.
Johnston DJ and Moore KL (2005) “Stocktake” – genetic audit software for Australian seedstock beef producers. Proceedings Association for the Advancement of Animal Breeding and Genetics 16, 161-164.
McWilliam SM, Lehnert SA and Reverter A (2005) Annotation analysis of a bovine cDNA microarray for expression profiling of muscle and adipose tissue. Proceedings Association for the Advancement of Animal Breeding and Genetics 16, 393-396.
Moore KL, Johnston DJ, Burrow HM (2005) Sire breed differences for net feed intake in feedlot finished beef cattle. Proceedings Association for the Advancement of Animal Breeding and Genetics 16, 76-79.
Pugh, A.K., McIntyre, B.L., Tudor, G. and Pethick, D.W. (2005).
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Understanding the effect of gender and age on the pattern of fat deposition in cattle. In: Indicators of milk and beef quality, J.F. Hocquette & S. Gigli (editors), EAAP publication No.112.pp405-408 Wageningen Academic Publishers.
Read DM, McIntyre BL, Taylor EG and Tudor GD (2005) Effect of time of calving and sire types on growth of progeny to weaning. Proceedings Association for the Advancement of Animal Breeding and Genetics 16, 342-345.
Wood BJ, van der Werf JHJ and Parnell PF (2005) Quantifying the selection response using a residual feed intake DNA marker for two Australian breeding objectives. Proceedings Association for the Advancement of Animal Breeding and Genetics 16, 169-172.
Non-refereed conference proceedings
Alcock, D., and Hegarty, RS (2005) Effects of pasture improvement on productivity, gross margin and methane emissions of grazing sheep enterprises. Proceedings of the 2nd International Greenhouse Gases and Animal Agriculture Conference, Zurich, Switzerland. 127-130.
Alford, AR, Cacho, OJ, Griffith, GR and Hegarty, RF (2006) “Jointly achieving profitability and environmental outcomes: methane abatement from genetic improvement in the Australian beef industry”, paper presented at the 50th annual conference of the Australian Agricultural and Resource Economics Society, Sydney, February 8-10.
Arthur PA, Herd RM, Johnston DJ, Wolcott ML and Barwick SA (2006) Genetics of growth and feed efficiency. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 53-64.
Arthur PF, Herd RM (2006) Selection for growth and feed efficiency - The Australian experience. Proceedings of the International Symposium on Recent Advances in Animal Sciences. Tohoku University, Sendai, Japan, November 2005, p18.
Bertram, J, R Farrell and V Edmondston (2005) Delivery of Beef CRC results in northern Australia. In “Moving from research to industry adoption” NSW DPI and Beef CRC Conference. May 2005. 53-55.
Bindon BM (2006) Achievements of the Beef CRC: A platform for the next 10 years. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 17-28.
Burrow HM, Johnston DJ, Thompson JM, Reverter A, Barwick SA and Perry D. (2006) Genetics of carcase and beef quality: take-home messages from the Beef CRC. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 69-78.
Burrow HM (2006) Outcomes and future research by the Beef Cooperative Research Centres in Australia. Proceedings 17th International Limousin Conference, 6 April 2006, Sydney, pp. 1-20.
Burrow HM (2006) Utilisation of diverse breed resources for tropical beef production. Proceedings 8th World Congress on Genetics Applied to Livestock Production (Invited paper, in press, 8 pages).
Clark R, Bacusmo J, Bond H, Gabunada F, Madzivhandila TP, Matjuda LE, Motiang DM, Nengovhela NB, Taveros AA, Timms J and Toribo J (2005) A model for achieving sustainable improvement and innovation in regions. Proceedings International Conference on Engaging Communities, Brisbane, Australia, August 2005.
Clark R, Timms J, Bacusmo J, Bond H, Espinosa E, Gabunada F, Madzivhandila TP, Matjuda LE, Motiang DM, Nengovhela NB and Toribio J (2005) Designing and managing R&D projects to achieve outcomes from the outset. Proceedings International Conference on Engaging Communities, Brisbane, Australia, August 2005.
Corrigan L and Parnell P (2006) Application of genetics technology in the temperate Australian beef seedstock industry. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 81-90.
CRC for Beef Genetic Technologies (2006) “Australian Beef – The Leader!” Conference Proceedings, 170 pages.
Cundiff LV (2006) The impact of quantitative genetics on productive, reproductive and adaptive traits in beef cattle. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 29-46.
Denman, SE, Tomkins, N, and McSweeney, CS, (2005) Monitoring the effect of bromochloromethane on methanogen populations within the rumen using qPCR. Proceedings of the 2nd International Greenhouse Gases and Animal Agriculture Conference, Zurich, Switzerland. 98-101.112-114.
Ferguson DM, Johnston DJ, Burrow HM and Reverter A (2006) Relationships between temperament, feedlot performance and beef quality. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 161-170.
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Fleming, P, Fleming, E, Rodgers, H, Griffith, G and Johnston, D (2005) “Animal efficiency in an intensive beef production system”, paper presented at the 11th Annual Congress of the European Association of Agricultural Economists, ‘The Future of Rural Europe in the Global Agri -Food System’, Copenhagen, Denmark, August 24-27.
Foster M (2006) The impact of science on the Australian feedlot sector and the flow of benefits to other sectors. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 149-152.
Frylinck L, Strydom PE and Scholtz MM (2005) Benchmarking the feedlot performance and meat quality of indigeneous genotypes in South Africa. Proceedings 4th All Africa Conference on Animal Agriculture Arusha, Tanzania
Garcia–Gonzalez, R, Yu, Z, Larue, RC, and Morrison, M (2005) PCR-DGGE analysis of prokaryote diversity and community structure in different fractions of rumen digesta. Proceedings of the 2005 Conference on Gastrointestinal Function, Chicago, IL.
Greenwood, P (2005) Consequences of Foetal Nutrition and Growth Retardation for Productivity of Ruminants. In: Report on joint FAO/IAEA consultants meeting on research needs for improvement of livestock productivity in developing countries through manipulation of nutrition in utero, and to identify future areas of research in animal nutrition, editors P. Greenwood, D. Poppi and H. Makkar. International Atomic Energy Agency, Vienna, Austria, 17-20 October 2005.
Greenwood, PL, Cafe, L, Hearnshaw, H, Hennessy, DW, Thompson, JM and Morris, SG (2006) Long-term consequences of birth weight and growth to weaning for carcass, yield and beef quality characteristics of Piedmontese- and Wagyu-sired cattle Australian Beef – the Leader! The impact of science on the beef industry. 7-8 March 2006. p.125.
Greenwood, PL and Oddy, VH (2006) How growth affects finishing growth and carcase and meat quality attributes. In: 2006 Armidale Feeder Steer School. Beef Quality CRC. Armidale 7-8 February 2006. (Presented by L.Cafe)
Greenwood, PL and Oddy, VH (2005). How growth affects finishing growth and carcase and meat quality attributes. In: Findings and outcomes of the Beef CRC. Nutrition, Meat Science & Health. CD II, version 1, July 2005, editors Brian Sundstrom and Bob Gaden. Beef Quality CRC. Armidale.
Greenwood, P, Poppi, D and Makkar, H (2005) Report on joint FAO/IAEA consultants meeting on research needs for improvement of livestock productivity in developing countries through manipulation of nutrition in utero, and to identify future areas of research in animal nutrition. International Atomic Energy Agency, Vienna, Austria, 17-20 October 2005.
Griffith, GR and Alford, AR (2005) “The US cattle cycle and Australian beef prices – June 2005”, Proceedings of the Emerald Beef School, The CRC for Cattle and Beef Quality, Queensland DPIF and Australian Agricultural College Corporation, Emerald, Queensland, July 12-14, pp.15-22.
Griffith GR (2006) Estimating the economic impact of a major beef industry research and development investment: the renewal of the Cooperative Research Centre for Beef Genetic Technologies. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 153-160.
Johnston DJ, Barwick SA, Burrow HM, Holroyd RG, Thompson JM, and Sullivan M (2005) Key design features and current status of CRC Project 2.3 – Links between the genetics of beef quality and components of herd profitability in northern Australia. NSW DPI Annual Beef Conference, Coffs Harbour.
Johnston DJ, Barwick SA, Holroyd RG, Fordyce G and Burrow HM (2006) Genetics of female reproduction traits. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 47-52.
Kinder JE, Osborne JM, Davis ME and Day ML (2006) Impact of reproductive technologies on improved genetics in beef cattle. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 141-146.
Matjuda LE and Scholtz MM (2005) Screening of indigenous cattle breeds for genetic markers. Proceedings 4th All Africa Conference on Animal Agriculture Arusha, Tanzania
McKiernan WA, Wilkins JF, Graham JF, Tudor GD, Deland MPB, McIntyre BL, Walkley JRW, Barwick SA and Irwin J (2006) CRC “Regional Combinations” Project – Regional beef systems to improve productivity and profitability. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 127-134.
Motiang DM, Matjuda LE, Clark R and Nengovhela NB (2005) Achieving sustainable livestock systems through partnerships: A case study of farmer teams in Limpopo and North West Provinces in South Africa. Proceedings International Conference on Agricultural Research for Development: European Responses to Changing Global Needs 27-29 April 2005, Swiss Federal Institute of Technology, ETH Zurich, Switzerland.
Motiang DM, Matjuda LE, Nengovhela NB and Clark R (2005) Partnerships do improve smallholder livestock systems: experience from Limpopo and North West Provinces in South Africa. Proceedings 4th All Africa Conference on Animal Agriculture Arusha, Tanzania.
Nengovhela NB (2005) Designing livestock poverty projects to achieve continuous improvement and sustainability: Kgalakgadi Dipudi enterprise review. Proceedings International Workshop on Improving the Well-being of Resource Poor communities - contribution of small livestock. 12-15 September 2005,Everglades Hotel, Howick, South Africa.
Nengovhela NB, Madzivhandila P, Motiang DM, Matjuda EL, Nenmbilwi D, Modise E, Mulaudzi JN, Rasebotsa S, Lukhele M, Banga C and Nesamvuni AE (2005). The outcome of using continuous improvement and innovation to improve livestock marketing for resource poor farmers in South Africa. Proceedings 4th All Africa Conference on Animal Agriculture Arusha, Tanzania.
Oddy VH (2006) The impact of science developed in the Beef CRCs on feeding and management practices in the Australian beef industry. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 137-140.
Ouwerkerk, D., Maguire, A.J., and Klieve, A.V. (2005) Reductive acetogenesis in the foregut of macropod marsupials in Australia. Proceedings of the 2nd International Greenhouse Gases and Animal Agriculture Conference, Zurich, Switzerland. 98-101.
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Pethick DW, Harper GS, Hocquette JF and Wang YH (2006) Marbling biology – what do we know about getting fat into muscle? Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 103-110.
Pethick, DW, Harper, GS, Hocquette, JF and Wang, Y (2006) Marbling biology - what do we know about getting fat into muscle? In Proceedings of ‘Australian beef – the leader ! The impact of science on the beef industry’ pp103-110. CRC for Beef Genetic Technologies, University of New England, Armidale, NSW, Australia
Polkinghorne R (2006) Guaranteed eating quality: making it work. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 121-124.
Timms J, Clark R, Espinosa E, Gabunada F, Madzivhandila TP, Maleza Z, Matjuda LE, McCartney A, Motiang DM, Nengovhela NB, Stewart P and Taveros AA (2005) Effective regional improvement and innovation networks. Proceedings International Conference on Engaging Communities, Brisbane, Australia, August 2005.
Prayaga KC, Corbet NJ, Henshall JM and Burrow HM (2006) Genetics of adaptive traits. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 65-68.
Reverter A, Ingham A, Lehnert SA, Tan SH, Wang YH, Ratnakumnr A and Dalrymple BP. (2006). A procedure for the simultaneous identification of differential gene expression and connectivity applied to inflammation, adipogenesis and cancer. The 2nd International Symposium on Animal Functional Genomics. Michigan State University, USA May 2006
Thompson JM, Perry D, Egan AF and Shorthose WR (2006) Guaranteed eating quality: the Australian science. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 111-120.
Thompson JM and Polkinghorne R (2006) Overview of MSA and the cuts based grading scheme. Proceedings 17th International Limousin Conference, 6 April 2006, Sydney, pp. 21-27.
Troy DJ, Mullen AM, Stapleton P, Brandon K and White AM (2006) The contribution of meat science to the development of a PACCP-based grading scheme for beef. Proceedings Australian Beef – The Leader! Conference, Beef CRC, Armidale 7-8 March 2006, pp. 97-102.
Wang YH, Reverter A, Harper GS, Mannen H, Taniguchi M, Oyama K and Lehnert SA (2005) Transcriptional profiling of intramuscular fat in growing beef cattle. ILSI’s 1st International Conference on Nutrigenomics, Singapore, December 7-9, 2005
Other publications
Alford, AR, Cacho, OJ and Griffith, GR (2006) A bio-economic model of a Northern Tablelands cattle grazing enterprise. I. Specification and validation of the model, Working Paper Series in Agricultural and Resource Economics No. 2006-2, Graduate School of Agricultural and Resource Economics, University of New England, Armidale, February.
Available online at: http://www.une.edu.au/economics/publications/GSARE/arewp06_2.pdf
Alford, AR, Cacho, OJ and Griffith, GR (2006) A bio-economic model of a Northern Tablelands cattle grazing enterprise. II. Application to evaluation of the net feed efficiency technology, Working Paper Series in Agricultural and Resource Economics No. 2006-3, Graduate School of Agricultural and Resource Economics, University of New England, Armidale, February.
Available online at: http://www.une.edu.au/economics/publications/GSARE/arewp06_3.pdf
Alford, AR, Cacho, OJ and Griffith, GR (2006) A bio-economic model of a Northern Tablelands cattle grazing enterprise. III. Alternative optimisation procedures, Working Paper Series in Agricultural and Resource Economics No. 2006-4, Graduate School of Agricultural and Resource Economics, University of New England, Armidale, February.
Available online at: http://www.une.edu.au/economics/publications/GSARE/arewp06_4.pdf
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Notes to Tables
Table 1a – Staff in-kind contributions from Participants and Supporting Participants
• The “in-kind” contributions from the Participants and Supporting Participants is calculated as the “Full Time Equivalent” (FTE) based on the percentage of time staff worked on CRC projects.
• The Animal Genetics and Breeding Units (AGBU), based at the University of New England, is funded jointly by the NSW Department of Primary Industries and the University of New England. The “in-kind” contributions from AGBU have been split between NSW Department of Primary Industries and the University of New England on a 50:50 basis.
• The projected in-kind contributions reflect the fact that much of the first year of operation of the CRC has been spent setting up the new Programs and Projects of research. Participants are expected to contribute staff to the CRC in line with the Commonwealth agreement over the next six years.
Table 1b – Non-staff in-kind contributions from Participants and Supporting Participants
• The non-staff in-kind contributions include overheads associated with Participant and Supporting Participant staff contributions to the CRC and the estimated cost of facilities utilised by the CRC. The amounts disclosed are estimated and reported to the CRC by Participants and Supporting Participants.
• Northern Pastoral Group non-staff in-kinds are now being contributed as cash contributions to the CRC on a reimbursement of expenditure basis associated with their experimental cattle maintained on Participant research stations.
• Projected non-staff in-kind contributions are expected to be in line with the Commonwealth Agreement with the exception of the Northern Pastoral Group contribution.
Table 2 – Participant Cash Contributions, Other Firm Cash and CRC Programme Funding
• The Participant Cash Contributions, Other Firm Cash and CRC Programme Funding table has been prepared on a cash basis and represents the funds received by the company from all sources.
• Cash contributions from several Participants are less than the amounts budgeted in Schedule 3 to the Commonwealth Agreement. The University of Queensland contribution has been received post year end. National Livestock Research Institute, Korea and Sygen International supporting participant agreements are under negotiation and budgeted contributions are expected to be received.
• The “Other Cash Resources” of $2.4 million comprised: funds transferred from the CRC for Cattle and Beef Quality of $1.1 million, GST received of $0.8 million, ACIAR grant of $0.3 million, Queensland State Development Grant of $0.1 million and interest income of $0.1 million.
• The Meat and Livestock Australia and Australian Lot Feeders Association cash contributions are gross contributions and include contributions funded from industry levies and matching Government funds.
• Projected cash contributions are expected to be in line with the Commonwealth Agreement.
Table 3 – Expenses
• The Expenses table has been prepared on an accruals basis.
• The Tullimba Cattle Research (Feedlot) Facility income and expenditure have been netted off within the financial tables to be consistent with the treatment of the facility in the Commonwealth Agreement where income earned by the facility is viewed as a reduction in the project cost for using the facility.
• The 2006-07 projected expenses are based on the year two operational plan which was approved by the Board in the June 2006 Board meeting. The 2007 to 2012 projections are expected to be inline with the Commonwealth Agreement.
Table 4 – Capital Items
• The Capital Items table has been prepared on a cash basis.
• Capital assets greater than $20,000 acquired during the year include: Farm Ute ($30k), Second Hand Tractor ($24k) and a Feed Mixer ($93k) for the Tullimba Cattle Research (Feedlot) Facility; CRC Centric web-based Project Management software ($30k); Ultrasound scanning system ($27k); and Tissue Lyser/Centrifuge ($20k) for the research programs. These assets have been funded from Participant contributions to the CRC, not from Commonwealth Grant funds.
• Due to the rapid technological developments in the genomics area, we have elected to outsource whole genome scans in Year 1 in lieu of capital purchases that could become redundant quickly. The Company may need to reconsider its capital expenditure in future years and purchase the capital equipment then. The projected capital expenditure reflects this outsourcing approach.
Table 5 – Allocation of Resources
• The Allocation of Resources table has been prepared on an accruals basis and the Tullimba Cattle Research (Feedlot) Facility income and expenditure have been netted off within the table.
• The projections are in line with the projections in tables 1a, 1b and 3.
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AUDITORS REPORT TO THE CO-OPERATIVE RESEARCH CENTRES PROGRAMDEPARTMENT OF SCIENCE EDUCATION AND TRAINING
REPRESENTING THE COMMONWEALTH IN RESPECT OFTHE CRC FOR BEEF GENETIC TECHNOLOGIES
FINANCIAL INFORMATION FORYEAR ENDED 30 JUNE 2006
SCOPE
The financial report and Director’s responsibilitiesWe have audited the financial information of the CRC for Beef Genetic Technologies as set out in Tables 1(a), 1(b), 2 , 3 and 4 of the Annual Report (being the tables showing the Number of Staff (FTE) , Total Non Staff In-Kind, Participants’ Cash Contributions, Other Firm Cash, CRC Programme Funding, Expenditure and Capital Items) for the year ended 30 June 2006. The Director’s of the Company are responsible for the preparation and presentation of the financial information. We have conducted an independent audit of the financial information in order to express an opinion on it to the Participants and Supporting Participants to the CRC for Beef Genetic Technologies and DEST.
The financial information has been prepared for the Participants and Supporting Participants to the CRC for Beef Genetic Technologies for the purposes of fulfilling their annual reporting obligations under clause 14.3 (vii) of the Commonwealth Agreement and for distribution to the Co-operative Research Centres Program, DEST, representing the Commonwealth of Australia. We disclaim any responsibility for any reliance on this report or on the financial information to which it relates to any person other than those mentioned above or for any purpose other than for which it was prepared.
Audit Approach
Our audit has been conducted in accordance with Australian Auditing Standards to provide reasonable assurance as to whether the financial information contained in Tables 1 to 4 is free of material misstatement. Our procedures included examination on a test basis, of evidence supporting the amounts and other disclosures in the financial information, and the evaluation of accounting policies and significant accounting estimates. These procedures have been undertaken to form an opinion whether, in all material respects, the financial information is presented fairly in accordance with Australian Accounting concepts and standards and requirements of the Commonwealth Agreement in terms of so as to present a view of the sources of funding , the application of funding and of the accrual based expenditure of the CRC for Beef Genetic Technologies which is consistent with our understanding of its financial activities during the year and its financial position as at 30 June 2006.
While we have not performed any audit procedures on the projections for the year ended 30 June 2007 or subsequent years and do not express any opinion thereon, we ascertained that they have been formally approved by the Board as required under Clause 9 of the Participants’ Agreement. The Board approved the 2007 Operational Plan at their June 2006 Board Meeting.
The audit opinion on these financial tables has been formed on the above basis.
79
Fin
anci
al R
ep
ort
AUDIT OPINION
In our opinion, the financial information presented in Tables 1 to 4 presents fairly the sources of funding, the application of funding, and the financial position of the CRC for Beef Genetic Technologies for the year ended 30 June 2006 in accordance with Australian Accounting Standards and the requirements of the Commonwealth Agreement in terms of Clauses 5 (Contributions), 6(1), 6(2) (a) (b) (c) (d)& (e), (Application of Grant and Contributions), 10(1), 10(5) (Intellectual Property) and 8 ( Accounting for Commonwealth Funding and Contributions).
Specifically:1. Each Researcher’s Contribution for the year under report has been provided at least to the value for the year
committed in the Budget as specified in Schedule 3 to the Agreement, with the following exceptions:
It should be noted that the above table shows the exceptions only against the Commonwealth Agreement.
The cash contribution from the University of Queensland has been received subsequent to balance date.
Year 1 Only
Participant
AmountCommittedCash &Non -StaffIn-Kind
AmountContributedCash &Non- StaffIn-Kind
VarianceTo AmountCommitted
AmountCommittedStaffIn-Kind
AmountContributed
StaffIn-Kind
VarianceTo AmountCommitted
$’000 $’000 $’000 FTE FTE FTECore ParticipantsDepartment of PrimaryIndustries and ResourcesSouth Australia 472 323 149 2.7 1.3 1.4
Department of PrimaryIndustries Victoria 258 63 195 3.2 3.5 0.3
The University ofQueensland 692 685 7 3.1 0.9 2.2
Genetic Solutions Pty Ltd 75 - 75 0.8 - 0.8
Murdoch University - - - 3.3 1.2 2.1
National LivestockResearch Institute, Korea
300 286 14 2.2 1.3 0.9
SASTEK Pty Ltd - - - 0.2 - 0.2
Sygen International 37 - 37 - - -
The Ohio State University,USA - - - 2 1.6 0.4
WA Department ofAgriculture - - - 4.8 2.3 2.5
�0
Fin
anci
al R
ep
ort
2. The Researcher has used the Commonwealth Grant and the Participants’ and Supporting Participants’ contributions for the activities of the Centre as set out in Schedule 3 to the Commonwealth Agreement and in my professional opinion there appear to be no material reporting irregularities.
Capital Items acquired from the Commonwealth Grant and Participants’ and Supporting Participants’ Contributions were listed in schedule 3 to the Commonwealth Agreement with the following exceptions:
Triton Ute $29,536 Tractor $26,500 Feed Mixer $93,316 Software License $30,000 Tissue Centrifuge $20,000
5. A statement signed by the Chief Executive Officer, to the effect that any Commercialisation or utilisation of Intellectual Property, including by any third party is undertaken in accordance with the Activities and the Commercialisation and Utilisation Plan described in Schedule 1 to the Commonwealth Agreement has been obtained by Roberts & Morrow.
6. The CRC has exercised proper accounting standards and controls. The income and expenditure in relation to the Activities are recorded separately from the other transactions of the Company. The cash contributions have been paid into and expended from the CRC’s account in accordance with Clause 8 to the Commonwealth Agreement. Tables 1, 2, 3 & 4 have been completed in accordance with the basis of preparation as outlined in the Notes to the Tables.
7. In accordance with Clause 13.4 of the Participants’ Agreement each participant is responsible for keeping separate documentation that records each non-cash Contribution. In relation to the audit of Table 1(b) Total Non- Staff In-Kind the scope of our audit testing has been limited to the information supplied by each participant to the Company in accordance with Clause 13.4 of the Participants’ Agreement. The Company has reported the information in this table based upon the information supplied to it by each Participant.
8. Table 5, Allocation of Resources, allocates Expenses, Non-Staff In-Kind. In-Kind-Staff (FTE) across each of the programmes. We have ensured that this table reconciles with the information as supplied in Tables 1 to 4 and is mechanically accurate but do not provide an opinion on the allocation of resources to the various programmes as this is considered by ourselves and the Board of Directors to be outside the scope of this audit.
ROBERTS & MORROWChartered Accountants
Michelle A PaullPartner29 September 2006137 Beardy StreetARMIDALE NSW 2350
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0.5
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0.2
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0.4
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0.2
0.2
0.2
0.2
0.2
0.2
0.2
0.2
0.2
0.2
0.6
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0.4
1.8
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2.7
2.7
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2.7
2.7
2.7
2.7
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Key
Res
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Man
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3.7
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3.8
3.8
3.8
3.8
3.8
3.8
3.8
3.8
3.8
3.8
3.8
3.8
3.7
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26.5
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Res
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3.2
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7.0
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7.0
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7.0
7.0
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7.0
7.0
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18.1
18.1
18.1
18.2
18.2
18.2
18.2
18.2
18.2
18.2
18.2
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3.8
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5.2
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5.2
5.2
5.2
5.2
5.2
5.2
5.2
5.2
5.2
5.2
3.8
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35.0
36.4
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Key
Res
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Man
ager
8.9
13.5
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13.5
13.5
13.5
13.5
13.5
13.5
13.5
13.5
13.5
13.5
13.5
13.5
8.9
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Res
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29.5
21.2
8.3
21.2
21.2
21.2
21.2
21.2
21.2
21.2
21.0
21.2
21.0
21.2
21.0
29.5
21.2
8.3
156.
714
7.8
8.9
Supp
ort
Staf
f10
.76.
64.
16.
66.
66.
66.
66.
76.
76.
76.
76.
76.
76.
76.
710
.76.
64.
150
.746
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1G
RA
ND
TOTA
L52
.946
.56.
446
.546
.546
.546
.546
.646
.646
.646
.446
.646
.446
.646
.452
.946
.56.
433
2.3
325.
37.
0
The
abov
eta
ble
isto
bere
adin
con
jun
ctio
nw
ith
the
not
esto
the
tabl
es
20
09
-10
20
10
-11
20
11
-12
20
05
-06
20
06
-07
20
07
-08
20
08
-09
Act
ual
Pro
ject
edTo
tals
to2
00
5-0
6To
tals
for
7ye
ars
�4
Fin
anci
al R
ep
ort
Tab
le �
b:
Fin
anci
al In
form
atio
n /
Tota
l No
n-S
taff
In-K
ind
($’0
00
s) (p
er p
arti
cip
ant)
Act
ual
Agr
'mt
Dif
f%
Dif
fP
roje
cted
Agr
'mt
Pro
ject
edA
gr'm
tP
roje
cted
Agr
'mt
Pro
ject
edA
gr'm
tP
roje
cted
Agr
'mt
Pro
ject
edA
gr'm
tA
ctu
alA
gr'm
tD
iff
%D
iff
Act
ual
/Pro
jAgr
'mt
Dif
f
CO
RE
PA
RTI
CIP
AN
TSD
ept
ofPr
imar
yIn
dust
ries
and
Res
ourc
esSA
273
422
-149
-35
423
423
423
423
423
422
423
423
423
422
423
423
273
422
-149
-35
2,81
12,
958
-147
Dep
artm
ent
ofPr
imar
yIn
dust
ries
Vict
oria
6325
8-1
95-7
625
825
825
825
825
825
825
825
825
825
825
825
863
258
-195
-76
1,61
11,
806
-195
Mea
tan
dLi
vest
ock
Aust
ralia
00
00
00
00
00
00
00
00
00
00
00
0M
eat
and
Woo
lNew
Zeal
and
00
00
00
00
00
00
00
00
00
00
00
0N
SWD
epar
tmen
tof
Prim
ary
Indu
strie
s92
766
925
839
669
669
669
669
669
669
669
669
669
669
669
669
927
669
258
394,
941
4,68
325
8Q
ldD
ept
ofPr
imar
yIn
dust
ries
and
Fish
erie
s91
685
957
785
985
985
985
985
985
985
985
985
985
985
985
991
685
957
76,
070
6,01
357
The
Uni
vers
ityof
Que
ensl
and
685
685
00
685
685
685
685
685
686
685
685
685
685
685
685
685
685
00
4,79
54,
796
-1U
nive
rsity
ofAd
elai
de62
754
384
1654
354
354
354
354
354
254
354
254
354
254
354
262
754
384
163,
885
3,79
788
Uni
vers
ityof
New
Engl
and
706
737
-31
-473
673
673
673
673
673
773
673
673
673
773
673
670
673
7-3
1-4
5,12
25,
155
-33
TOTA
LC
OR
EP
AR
TIC
IPA
NTS
4,19
74,
173
241
4,17
34,
173
4,17
34,
173
4,17
34,
173
4,17
34,
172
4,17
34,
172
4,17
34,
172
4,1
97
4,1
73
24
12
9,2
35
29
,20
82
7
SU
PP
OR
TIN
GP
AR
TIC
IPA
NTS
Aust
ralia
nLo
tFe
eder
sAs
soci
atio
n0
00
00
00
00
00
00
00
00
00
00
00
CSIR
OLi
vest
ock
Indu
strie
s1,
113
828
285
3482
882
882
882
882
882
882
882
882
882
882
882
81,
113
828
285
346,
081
5,79
628
5G
enet
icSo
lutio
nsPt
yLt
d0
75-7
5-1
0075
7575
7575
7575
7575
7575
750
75-7
5-1
0045
052
5-7
5M
urdo
chU
nive
rsity
500
490
102
490
490
490
490
490
490
490
491
490
491
490
491
500
490
102
3,44
03,
433
7N
atio
nalL
ives
tock
Res
earc
hIn
stitu
te,K
orea
286
286
00
286
286
286
286
286
286
286
286
286
286
286
286
286
286
00
2,00
22,
002
0N
orth
ern
Past
oral
Gro
upof
Com
pani
es0
214
-214
-100
021
40
214
021
40
214
021
40
215
021
4-2
14-1
000
1,49
9-1
,499
SAST
EKPt
yLt
d0
00
00
00
00
00
00
00
00
00
00
00
Syge
nIn
tern
atio
nal
00
00
00
00
00
00
00
00
00
00
00
0Th
eO
hio
Stat
eU
nive
rsity
,USA
346
286
6021
286
286
286
286
286
286
286
286
286
286
286
286
346
286
6021
2,06
22,
002
60W
AD
epar
tmen
tof
Agric
ultu
re12
012
00
012
012
012
012
012
012
012
012
012
012
012
012
012
012
00
084
084
00
TOTA
LS
UP
PO
RTI
NG
PA
RTI
CIP
AN
TS2,
365
2,29
966
32,
085
2,29
92,
085
2,29
92,
085
2,29
92,
085
2,30
02,
085
2,30
02,
085
2,30
12
,36
52
,29
96
63
14
,87
51
6,0
97
-1,2
22
OTH
ERN
ON
-STA
FFIN
-KIN
DR
ESO
UR
CES
00
00
00
00
00
00
00
00
00
00
00
0
GR
AN
DTO
TAL
6,56
26,
472
901
6,25
86,
472
6,25
86,
472
6,25
86,
472
6,25
86,
472
6,25
86,
472
6,25
86,
473
6,56
26,
472
901
44,1
1045
,305
-1,1
95
The
abov
eta
ble
isto
bere
adin
con
jun
ctio
nw
ith
the
not
esto
the
tabl
es
Act
ual
Pro
ject
edTo
tals
to2
00
5-0
6To
tals
for
7ye
ars
20
09
-10
20
10
-11
20
11
-12
20
05
-06
20
06
-07
20
07
-08
20
08
-09
�5
Fin
anci
al R
ep
ort
Tab
le �
: Fi
nan
cial
Info
rmat
ion
/ P
arti
cip
ants
Cas
h C
on
trib
uti
on
s, O
ther
Fir
m C
ash
an
d C
RC
Pro
gra
mm
e Fu
nd
ing
($’0
00
s) c
on
tin
ued
...
Act
ual
Agr
'mt
Dif
f%
Dif
fP
roje
cted
Agr
'mt
Pro
ject
edA
gr'm
tP
roje
cted
Agr
'mt
Pro
ject
edA
gr'm
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roje
cted
Agr
'mt
Pro
ject
edA
gr'm
tA
ctu
alA
gr'm
tD
iff
%D
iff
Act
ual
/Pro
jA
gr'm
tD
iff
CO
RE
PA
RTI
CIP
AN
TSD
epar
tmen
tof
Prim
ary
Indu
strie
san
dR
esou
rces
5050
00
5050
5050
5050
5050
5050
5050
5050
00
350
350
0D
epar
tmen
tof
Prim
ary
Indu
strie
sVi
ctor
ia0
00
00
00
00
00
00
00
00
00
00
00
Mea
tan
dLi
vest
ock
Aust
ralia
1,03
450
053
410
71,
100
500
1,10
050
01,
100
500
1,10
050
01,
100
500
1,10
050
01,
034
500
534
107
7,63
43,
500
4,13
4M
eat
and
Woo
lNew
Zeal
and
293
293
00
293
293
293
293
293
293
293
293
293
293
293
293
293
293
00
2,05
12,
051
0N
SWD
epar
tmen
tof
Prim
ary
Indu
strie
s38
1325
192
012
013
00
00
00
00
3813
2519
238
380
Que
ensl
and
Dep
artm
ent
ofPr
imar
yIn
dust
ries
and
3813
2519
20
120
130
00
00
00
038
1325
192
3838
0Th
eU
nive
rsity
ofQ
ueen
slan
d0
7-7
-100
147
77
77
77
77
88
07
-7-1
0050
500
Uni
vers
ityof
Adel
aide
100
100
00
100
100
100
100
100
100
100
100
100
100
100
100
100
100
00
700
700
0U
nive
rsity
ofN
ewEn
glan
d38
1325
192
013
012
00
00
00
00
3813
2519
238
380
TOTA
LC
OR
EP
AR
TIC
IPA
NTS
'CA
SH
1,59
198
960
261
1,55
798
71,
550
988
1,55
095
01,
550
950
1,55
095
01,
551
951
1,59
198
960
261
10,8
996,
765
4,13
4
SU
PP
OR
TIN
GP
AR
TIC
IPA
NTS
Aust
ralia
nLo
tFe
eder
sAs
soci
atio
n12
060
6010
012
060
120
6012
060
120
6012
060
120
6012
060
6010
084
042
042
0CS
IRO
Live
stoc
kIn
dust
ries
3813
2519
20
130
120
00
00
00
038
1325
192
3838
0G
enet
icSo
lutio
nsPt
yLt
d0
00
00
00
00
00
00
00
00
00
00
00
Mur
doch
Uni
vers
ity0
00
00
00
00
00
00
00
00
00
00
00
Nat
iona
lLiv
esto
ckR
esea
rch
Inst
itute
,Kor
ea0
14-1
4-1
0028
1414
1413
1314
1413
1314
130
14-1
4-1
0096
951
Nor
ther
nPa
stor
alG
roup
ofCo
mpa
nies
242
024
20
358
030
00
300
030
00
00
024
20
242
01,
500
01,
500
SAST
EKPt
yLt
d0
00
00
00
00
00
00
00
00
00
00
00
Syge
nIn
tern
atio
nal
037
-37
-100
7638
3737
3838
3838
3838
3838
037
-37
-100
265
264
1Th
eO
hio
Stat
eU
nive
rsity
,USA
00
00
00
00
00
00
00
00
00
00
00
0W
AD
epar
tmen
tof
Agric
ultu
re0
00
00
00
00
00
00
00
00
00
00
00
TOTA
LS
UP
PO
RTI
NG
PA
RTI
CIP
AN
TS'C
AS
H40
012
427
622
358
212
547
112
347
111
147
211
217
111
117
211
140
012
427
622
32,
739
817
1,92
2
OTH
ERC
AS
HO
ther
Cash
Res
ourc
es2,
436
02,
436
090
00
00
00
00
00
00
2,43
60
2,43
60
3,33
60
3,33
6CR
CPr
ogra
mm
eFu
ndin
g4,
500
4,50
00
06,
000
6,00
05,
700
5,70
05,
100
5,10
04,
200
4,20
03,
000
3,00
01,
500
1,50
04,
500
4,50
00
030
,000
30,0
000
TOTA
LO
THER
CA
SH
6,93
64,
500
2,43
654
6,90
06,
000
5,70
05,
700
5,10
05,
100
4,20
04,
200
3,00
03,
000
1,50
01,
500
6,93
64,
500
2,43
654
33,3
3630
,000
3,33
6
TOTA
LC
AS
H8,
927
5,61
33,
314
599,
039
7,11
27,
721
6,81
17,
121
6,16
16,
222
5,26
24,
721
4,06
13,
223
2,56
28
,92
75
,61
33
,31
45
94
6,9
74
37
,58
29
,39
2
The
abov
eta
ble
isto
bere
adin
con
jun
ctio
nw
ith
the
not
esto
the
tabl
es
Act
ual
Pro
ject
edTo
tals
to2
00
5-0
6To
tals
for
7ye
ars
20
09
-10
20
10
-11
20
11
-12
20
05
-06
20
06
-07
20
07
-08
20
08
-09
�6
Fin
anci
al R
ep
ort
Tab
le �
: Fi
nan
cial
Info
rmat
ion
/ Ex
pen
ses
(Acc
rual
) ($
’00
0s)
Act
ual
Agr
'mt
Dif
f%
Dif
fP
roje
cted
Agr
'mt
Pro
ject
edA
gr'm
tP
roje
cted
Agr
'mt
Pro
ject
edA
gr'm
tP
roje
cted
Agr
'mt
Pro
ject
edA
gr'm
tA
ctu
alA
gr'm
tD
iff
%D
iff
Act
ual
/Pro
jA
gr'm
tD
iff
Empl
oyee
Expe
nses
2,03
11,
929
102
53,
711
2,57
42,
444
2,44
42,
186
2,18
61,
800
1,80
01,
286
1,28
664
364
32,
031
1,92
910
25
14,1
0112
,862
1,23
9Su
pplie
rEx
pens
es4,
165
2,24
31,
922
865,
287
3,22
43,
180
3,18
02,
874
2,87
42,
365
2,36
51,
698
1,69
884
984
94,
165
2,24
31,
922
8620
,418
16,4
333,
985
Oth
erEx
pens
es77
1,74
8-1
,671
-96
02,
456
2,44
22,
442
2,14
32,
143
1,81
01,
810
1,26
61,
266
643
643
771,
748
-1,6
71-9
68,
381
12,5
08-4
,127
TOTA
LEX
PEN
SES
6,27
35,
920
353
68,
998
8,25
48,
066
8,06
67,
203
7,20
35,
975
5,97
54,
250
4,25
02,
135
2,13
56
,27
35
,92
03
53
64
2,9
00
41
,80
31
,09
7
The
abov
eta
ble
isto
bere
adin
con
jun
ctio
nw
ith
the
not
esto
the
tabl
es
Act
ual
Pro
ject
edTo
tals
to2
00
5-0
6To
tals
for
7ye
ars
20
09
-10
20
10
-11
20
11
-12
20
05
-06
20
06
-07
20
07
-08
20
08
-09
Tab
le 4
: Fi
nan
cial
Info
rmat
ion
/ C
apit
al It
ems
($’0
00
s)
Act
ual
Agr
'mt
Dif
f%
Dif
fP
roje
cted
Agr
'mt
Pro
ject
edA
gr'm
tP
roje
cted
Agr
'mt
Pro
ject
edA
gr'm
tP
roje
cted
Agr
'mt
Pro
ject
edA
gr'm
tA
ctu
alA
gr'm
tD
iff
%D
iff
Act
ual
/Pro
jAgr
'mt
Dif
fTO
TAL
EXP
END
ITU
RE
224
500
-276
-55
4128
575
7520
2020
200
00
022
450
0-2
76-5
538
090
0-5
20
The
abov
eta
ble
isto
bere
adin
con
jun
ctio
nw
ith
the
not
esto
the
tabl
es
Act
ual
Pro
ject
edTo
tals
to2
00
5-0
6To
tals
for
7ye
ars
20
09
-10
20
10
-11
20
11
-12
20
05
-06
20
06
-07
20
07
-08
20
08
-09
�7
Fin
anci
al R
ep
ort
Tab
le 5
: Fi
nan
cial
Info
rmat
ion
/ A
lloca
tio
n o
f Res
ou
rces
Act
ual
Agr
'mt
Dif
f%
Dif
fA
ctu
alA
gr'm
tD
iff
%D
iff
Act
ual
Agr
'mt
Dif
f%
Dif
f
PR
OG
RA
MM
ER
esea
rch
Prog
ram
me
11,
352
953
399
421,
891
1,39
349
836
12.6
8.2
4.4
53.7
Res
earc
hPr
ogra
mm
e2
1,07
887
720
123
1,81
81,
292
526
419.
78.
21.
518
.8R
esea
rch
Prog
ram
me
325
576
8-5
13-6
776
21,
180
-418
-35
3.1
7.5
-4.4
-58.
5R
esea
rch
Prog
ram
me
41,
272
989
283
291,
596
1,47
412
28
16.2
9.4
6.8
72.3
Educ
atio
nPr
ogra
mm
e20
246
5-2
63-5
712
148
5-3
64-7
50.
52.
4-1
.9-7
9.2
Com
mer
cial
isat
ion
808
1,24
5-4
37-3
531
832
4-6
-210
.69.
41.
213
.1Ad
min
istr
atio
n1,
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9�
Glo
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Glossary
9�
Glo
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Glossary
TERM DEFINITIONACIAR Australian Centre for International Agricultural Research, an Australian research
funding agency that uses Australian research capacity to solve agricultural research problems in developing countries.
AGBU Animal Genetics and Breeding Unit, based at UNE Armidale, a joint venture of NSW Agriculture and the University of New England.
ALFA Australian Lot Feeders’ Association represents feedlots in Australia at every level, as the industry’s national peak body.
allele One variant of a gene.ARC Australian Research CouncilARI QDPI’s Animal Research Institute, YeerongpillyBeef-N-omics A decision support system developed by NSW Agriculture for southern beef
production systems, which combines herd dynamics, pasture availability and gross margin budgets. To be used in Project 5.5.
bioinformatics The computational and mathematical background to modern biology and genomics; bioinformaticians can be database specialists, statisticians or computer programmers.
biopsy Removal and examination of tissue, cells or fluids from the living body.Bos indicus Breeds of cattle originating from the Indian sub-continent; sometimes called Zebu
breeds and includes Brahman and Sahiwal.Bos taurus Temperate British and European breeds of cattle e.g. Hereford, Angus, Charolais.BREEDOBJECT A computer software package used to derive beef breeding objectives by weighting
traits in the selection program for their relative economic values.BREEDPLAN Australia’s beef genetic evaluation system, that estimates breeding values for
economically important traits.cohort See management groupcollagen An insoluble fibrous protein that occurs in vertebrates as the chief constituent of the
fibrils of connective tissue and of the organic substance of bones.composite A breed resulting from the matings of two or more existing breeds and animals are
selected from within the progeny to continue the breed (e.g. Belmont Red, Santa Gertrudis).
connective tissue The sinuous material that runs between muscle cells and binds them together. In the concentrated and cooked form it is the gristle in meat.
CRC Cooperative Research CentreCSIRO Commonwealth Scientific and Industrial Research OrganisationDNA Deoxyribonucleic acid, containing the genetic information that is passed from one
generation to the next. It is a long, usually double-stranded molecule made up of nucleotides G, A, T and C.
DNA fingerprinting A method of determining the parentage of animals using DNA extracted from samples such as blood or tissue obtained from the animals. Each animal has a unique genetic makeup (DNA fingerprint). By comparing the DNA fingerprint of progeny with potential parents it is possible to determine actual parentage.
9�
Glo
ssar
y
TERM DEFINITIONDNA marker Gene markers are used to detect different forms of genes. Tests based on gene
markers are used to predict the breeding performance, and in some cases the lifetime performance of animals with respect to specific traits. The tests can be carried out on a wide range of tissue samples such as blood, skin, hair or muscle collected at any age after conception.
DPI Department of Primary Industriesdressing percentage Ratio of carcase weight to preslaughter live weight.EBV Estimated Breeding Value, an estimate of an animal’s genetic value for measurable
traits such as growth rate, meat tenderness etc. EBVs are calculated from the measured performance of animals and their close relatives relative to other animals managed in an identical way.
EMA Eye muscle areaEMAI Elizabeth Macarthur Agricultural Institute. NSW Department of Primary Industries in
Sydney.EST “expressed sequence tag”: a short (several hundred bases) nucleotide sequence
derived from one end of a cDNA clone; usually serves to determine the likely identity of the cDNA clone.
flight time A measure of temperament of animals, it is the electronically-recorded time taken (in hundredths of a second) for an animal to cover a fixed distance (1.7 to 2.2 metres) after leaving a weighing crush.
gene The basic unit of heredity. Each gene has two or more forms which can be the same or different.
gene expression The process by which a gene code is transcribed into messenger RNA and exported to the nucleus for translation into proteins; gene expression can be studied by analysing the population of cytoplasmic RNAs.
gene marker See DNA marker.genetic correlation Extent to which two attributes are determined by the same genes. Genetic correlations
range from -1.00 to +1.00. A high negative relationship means an increase in one trait leads to a decrease in the other; a high positive relationship indicates an increase in one trait leads to an increase in the other trait. A low or zero correlation indicates there is little genetic relationship between the two traits.
heritability Proportion of variation for a measurable trait attributable to variation in genetic factors and is therefore passed on to offspring. Heritabilities (h2) range from 0.0 to 1.0. An h2 = 0 means the trait is not controlled by genetic factors and h2 = 1 means the trait is under total genetic control. In general, traits that have h2 > 0.4 are considered to be highly heritable.
HGP Hormonal growth implantIGF-I Insulin-like Growth Factor 1 - a factor which can be measured in blood and has been
shown to be associated with feed efficiency and fatness traits.in vitro Literally, ‘in glass’, and it refers to experiments that mimic life in a test tube or by
tissue culture.in vivo Examining the reactions of life, by experimentation with the living animal.
94
Glo
ssar
y
TERM DEFINITIONmanagement group A management group comprises a group of animals receiving identical treatment
for the duration of the evaluation. For BREEDPLAN evaluations, this means that animals are born in the same paddock over the same time period and are exposed to the same management routines (supplementary feeding, weaning times etc.) throughout the period of the evaluation.
MLA Meat and Livestock AustraliaMSA Meat Standards Australia, Australia’s new meat grading scheme based on guaranteed
eating quality.Net Feed Intake (NFI) Net Feed Intake (NFI) A measure of feed efficiency that refers to variation in feed
intake between animals remaining after differences due to weight and growth rate have been accounted for. Low (more negative) NFI is desirable.
P8 fat thickness Fat thickness in mm recorded at the P8 rump site.PCR Polymerase chain reaction, a technique to amplify DNA strands and used as a
diagnostic tool to detect the presence of particular genetic sequences e.g. to identify a particular bacteria or a virulence factor in a bacteria.
peak force See Shear forcepH pH value of meat sample, calculated as the mean of 4 measurements using a probe-
type combined electrode (normal values 5.5 to 5.7).phenotype The appearance, structure or biochemical characteristics of an organism, contrasted
against genotype, which refers to sequences within the DNA.polymorphic Having many forms. In this context, it refers to multiple forms of a gene that lead to
slight but measurable variation in a phenotype. Also relates to the various forms in which fat crystallises.
polymorphism The situation where more than one allele or variant of a gene is found in a population.
QDPI&F Qld Department of Primary Industries and FisheriesRBY% Retail beef yield percentage – is generally referred to when carcasses are boned out
to commercial standards and trim. RBY% - saleable meat divided by cold carcass weight multiplied by 100.
rib fat thickness Fat thickness in mm recorded at the 12/13th rib site.RNA Ribonucleic acid: the string of nucleotides (ususally single-stranded) that is
“transcribed” from DNA.RT-PCR Real time PCRSanga Adapted Bos taurus breeds that evolved in Southern Africa independent of the
European Bos taurus. They retain the productive attributes of the European Bos taurus but have resistance closer to that of the Bos indicus.
SARDI South Australian Research and Development Institutesequencing DNA, RNA, protein or oligosaccharide structure determination.shear force An objective measure of meat toughness, measured as the force required to sever
the muscle fibres of a meat sample (measured in kgs, with the higher the value, the tougher the meat).
SNP Single nucleotide polymorphism. A polymorphism at a specific base or nucleotide in the DNA sequence. For instance, at a point in the DNA sequence where one allele contains an ’A’, another allele contains a ‘T’.
trait Attribute or characteristic of animals that can be improved genetically (for example, growth rate, fertility, carcase or meat quality etc).
UC-Davis University of California - DavisUNE University of New EnglandUSDA United States Department of Agriculture
Established and supported under the Australian Government’s Cooperative Research Centres Program
Proudlysupportedby
CJ Hawkins Homestead, University of New England, Armidale NSW 2351p 02 6773 3501 • f 02 6773 3500 • e [email protected] • w www.beefcrc.com.au
The Beef Cooperative Research Centre (Beef CRC) is Australia’s largest integrated beef research program bringing together leading beef researchers from across Australia along with prestigious national and international beef industry partners and biotechnology businesses.
The world class research underway by the Beef CRC aims to increase profits for Australia’s cattle industry by at least $179 million per annum from 2012.
To do this, the Beef CRC is focusing on gene discovery and gene expression which will create precision breeding and management strategies to improve profitability for all sectors of the Australian beef industry - breeding, growing, finishing, processing and retailing.
Aboutus
Rockhampton
Brisbane
Armidale (Beef CRC HQ)
Melbourne
AdelaidePerth
Wellington
Beef CRC Major Research Sites
Research StationsBelmont, Qld
Brian Pastures, QldBrigalow, Qld
Swans Lagoon, QldToorak, Qld
Glen Innes, NSWTrangie, NSW
Tullimba, NSWHamilton, Vic
Struan, SAVasse, WA
Contactus
Established and supported under the Australian Government’s Cooperative Research Centres Program
Cooperative Research Centre forBeef Genetic Technologies
ANNUALREPORT2005/2006
World class science, creating first class beef
CO
OPER
ATIVE RESEA
RC
H C
ENTRE FO
R BEEF G
ENETIC
TECH
NO
LOG
IES AN
NU
AL REPO
RT 2005/2006