1

Comprehensive abattoir chiller assessment and meat science information is being collected within the progeny test programs being conducted by several

breed societies as part of the Beef Information Nucleus (BIN) and is providing valuable information relating to the genetic differences between sires for various carcase composition and eating quality attributes.

Beef Information Nucleus progeny test programs are presently being conducted by Angus Australia, the Australian Brahman Breeders Association, the Charolais Society of Australia, Herefords Australia, the Australian Limousin Breeders Society and the Australia Wagyu Association with the assistance of funding from Meat & Livestock Australia (MLA) Donor Company, participating co-operator herds, bull suppliers and various industry partners.

Within the BIN programs, elite sires in each breed are evaluated in a structured progeny test program in co-operator herds located across Australia. All progeny are comprehensively performance recorded across a range of commercially important traits, which in turn collects valuable information regarding the genetics of each sire.

In the case of carcase attributes, progeny are measured for eye muscle area, fat depth and intramuscular fat via live animal ultrasound scanning and then traced through the abattoir where comprehensive chiller assessment measurements are collected. Abattoir measurements vary slightly between the different programs and abattoirs but include such traits as carcase weight, eye muscle area, fat depth, meat colour, fat colour, marble score (AUSMEAT and MSA), hump height, ossification, pH, butt shape and carcase value.

Meat samples are also collected from each carcase and sent to the meat science laboratory at the University of New England

Comprehensive Carcase Information Being Collected within Beef Information Nucleus

in Armidale for further analysis. Meat science laboratory measurements are collected for a range of eating quality attributes such as intramuscular fat, shear force (tenderness), cooking loss and meat colour.

Abattoir carcase information is being collected on all progeny within the Charolais and Limousin programs, whereas

“SBTS & TBTS provide A national extension network for

genetic technologies for the Australian beef seedstock industry”

UPDATE

WINTER

2014

Comprehensive chiller assessment and meat sciencemeasurements are being collected on progeny within the

Beef Information Nucleus.

2

UPDATE

WINTER

2014information is only collected on steer progeny within the Angus, Brahman and Hereford programs as female progeny are being retained for breeding.

The progeny test programs represent a significant commitment by each participating breed organisation in striving for continuous improvement in profitability through investment in performance recording and application of genetic technologies. This investment includes a significant commitment to research and development, particularly to generate the potential to achieve genetic improvement in difficult to measure traits such as carcase composition and eating quality.

In addition to providing valuable information on genetic differences between elite sires for carcase attributes through inclusion in routine BREEDPLAN genetic evaluations, the information being collected within the BIN programs will provide a valuable R&D resource for the possible future development of genomic breeding values. This information will contribute to the ongoing improvement of carcase composition and eating quality within the Australian beef herd, particularly within those breeds actively participating in BIN progeny test programs.

in this issue

Comprehensive CarcaseInformation Being Collectedwithin Beef Information Nucleus 1

New Technical Areas NowAvailable on the SBTS andTBTS Websites 2

Enhancements to AngusGROUP BREEDPLAN 3

Genetic Improvement ofTemperament 4

BullSELECT WorkshopsProve Popular 6

Understanding the EBVPercentile Graph 7

“Getting Started with BREEDPLAN”Area Now Available 7

Using Male Reproduction Traitsto Improve Female Reproductionin Tropical Cattle 8

Increasing Pedigree Accuracywith DNA Parent Verification 10

Docility EBVs Now Available forHereford and Simmental Animals 12

Recording Docility Scores forBREEDPLAN 13

Enhancements Made to HerefordGROUP BREEDPLAN 14

Follow SBTS & TBTS onSocial Media 15

Staff Departures - Christian Duffand Andrew Byrne 15

Staff Movements - Gemma WilkinsonNow Based in Southern NSW 15

Accessing Support in Applicationof Genetic Technologies 16

New Technical Areas Now Available on the SBTS and TBTS Websites

The SBTS and TBTS websites have recently been updated with the establishment of a specific “DNA Resources” area. The DNA Resources area has been compiled as a resource guide for producers considering the use and application

of DNA technology within their seedstock enterprise.

A specific “Breeding for Fertility” area has also been established on the TBTS website as a central resource for producers considering genetic selection for fertility traits and contains a range of useful technical documents.

The new web pages will be routinely updated as new information comes to hand and can be accessed from Technical Documents links on the SBTS (http://sbts.une.edu.au) and TBTS (http://tbts.une.edu.au) homepages.

Continued - Comprehensive Carcase Information Being Collected within Beef Information Nucleus

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Anumber of significant enhancements were implemented into the BREEDPLAN software that is used to calculate EBVs for Angus animals within

the April 2014 Angus GROUP BREEDPLAN analysis. These enhancements are part of the routine maintenance of the BREEDPLAN software and have resulted in the calculation of improved BREEDPLAN EBVs for Angus animals. The enhancements include:

Revisions to the main multi-trait analysis

The main multi-trait model used in the Angus BREEDPLAN analysis has been revised to include several enhancements:

> Revised adjustment factors - differences in performance records are adjusted for non-genetic differences such as differences in the age of the animal, the age of the dam and for carcase traits other than weight, differences in carcase weight. The adjustment factors that are used have been re-estimated to ensure adjustments remain appropriate for the performance information being analysed.

> Revised genetic parameters - the calculation of EBVs requires information on the genetic variation expressed in each trait, as well as the correlations between all traits. All trait heritabilities and correlations have been re-estimated to ensure that the genetic parameters remain appropriate for the performance records being analysed.

> Revised definition of carcase traits - with the exception of carcase weight, all carcase EBVs are now expressed as differences in a standard 400 kg steer carcase, while carcase weight EBVs are now expressed as differences at 750 days of age. This increase in weight (from 300 kg) and age (from 650 days) has little effect on the ranking of animals for the carcase EBVs but was necessary in order to appropriately analyse the recent abattoir carcase information being submitted to BREEDPLAN, where the average weight and age of carcases has increased substantially.

> Inclusion of net feed intake - the two trial net feed intake EBVs currently reported for Angus animals, NFI-p (post-weaning) and NFI-f (finishing) are now calculated as part of the main multi-trait analysis. Previously, these EBVs were calculated as part of a separate analysis. This change means that NFI EBVs are now calculated and available for all animals in the main Angus BREEDPLAN analysis, providing their EBVs meet minimum accuracy reporting thresholds.

Enhancements to AngusGROUP BREEDPLAN

Revised genetic parameters for the calving ease analysis The genetic parameters used in the calving ease analysis have been re-estimated to ensure they remain appropriate for the records being analysed. The direct and maternal variances and heritabilities for calving ease have increased, creating more spread in the EBVs. More influence has also been given to both birth weight and gestation length in the calculation of calving ease EBVs.

Addition of new abattoir carcase dataImplementation of the revised adjustment factors and genetic parameters for carcase traits now makes possible the inclusion of a significant amount of abattoir carcase information that has been collected on Angus animals with heavier carcase weights.

Update to base year

The base year used within the Angus BREEDPLAN analysis has been updated from 1995 to 2005. The change to the base year will not have an effect on the EBVs of individual animals but has been made to provide a more appropriate base population. The base population acts like an “anchor” point in the analysis. A base adjustment has also been made to each of the selection indexes to bring the new average values in line with the old average values for more recent animals (eg. 2012 born calves).

Implications for selection index values

Although no changes have been made to the production scenarios used in the calculation of the selection index values, the underlying genetic parameters within the BreedObject software have been changed to reflect those now used in the main Angus BREEDPLAN analysis. This has resulted in changes to the EBV weightings being used in the calculation of the selection index values.

If you have any questions regarding the enhancements to Angus BREEDPLAN, please contact Carel Teseling at Angus Australia on (02) 6773 4602.

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Temperament (also known as docility) is described as the way that cattle behave when confined in yards or put in an unusual situation such as being separated

from the mob. What we define as poor temperament is a survival trait in the wild – fear of anything unusual and the desire to escape. In domesticated cattle it can be exhibited as flight, or at its extreme fight.

Temperament is an important trait in beef herds with poor temperament having considerable impact on the profitability of the beef enterprise. Among other things, poor temperament in cattle will:n Increase production costs.n Make cattle harder to muster and handle.n Damage infrastructure e.g. yards and fences.n Increase risk of injury and stress to cattle.n Increase risk of injury and stress to stock handlers.n Increase weight loss during transit.n Lower feedlot performance.n Increase risk of dark cutters in the chiller. It’s estimated

that dark cutting beef costs the Australian Beef Industry in excess of $35 million annually.

n Lower eating quality (tougher beef ).

While different management techniques can be used to improve the overall temperament of a herd (e.g. yard weaning of calves), temperament is a highly heritable trait which can be improved in both the short and long term through genetic selection. There are also no known antagonistic genetic relationships with other traits of importance, enabling temperament to be improved genetically without impacting negatively on other traits.

Improvement of the genetics for temperament through genetic selection is of particular importance to seedstock producers.

Genetic Improvement of Temperament

Talk to any savvy bull buyer and a trait up the top of their bull buying checklist will be good temperament or good docility. This relates to their bull purchase having acceptable temperament themselves, and also to the ability of the bull to sire progeny within their herd with acceptable temperament.

Assessing Animal TemperamentWhile it is common practice to observe animals and assess their temperament when they are being handled, there are several methods of more formally measuring the temperament of animals.

Collection of Docility Scores Docility scores, being the subjective assessment of animals’ temperament, are recorded on animals at weaning or shortly afterwards. The advantage of scoring at weaning is that all calves should have had minimal handling and so will express variation in temperament. Variation in handling between animals prior to scoring should also be minimised.

Docility scores are collected on animals using either a yard or crush test:n Yard Test - The calves are individually put into a small

square yard and the handler attempts to hold the animal in one corner for about 30 seconds.

n Crush Test - The calves are put up a race and held in a crush or weigh scales for about 30 seconds but not head bailed.

When using the crush or yard test, the behaviour of animals is observed and animals scored on a 1-5 scale, with 1 being ‘docile’ and 5 being ‘aggressive’.

More detailed information regarding the collection of docility scores is provided in the article on page 13.

In domesticated cattle poor temperament can be exhibited as fight or flight.

5

Measurement of Flight Time

Flight time measurements are recorded on animals using specialised flight time equipment. Animals are held individually in the crush for a short period and then the head bail opened. Two light beams are then used to objectively measure the time taken for the animal to travel approximately 2.0 metres at the exit of the crush (Figure 2). Similar to docility scores, flight time measurements are normally recorded early in an animal’s life, usually at or around weaning.

While both methods have proven to be useful measures of an animal’s temperament, it is currently common practice for the tropical beef breeds to measure temperament through collection of flight time measurements due to its genetic relationship with beef tenderness in tropical breeds. Conversely, British and European breeds more commonly record docility scores due to there being no requirement for specialised equipment when using the subjective scoring system while still providing a high heritability for the trait.

Calculation of Estimated Breeding Values (EBVs) for Temperament

Additional to the collection of docility score or flight time information, several breeds now produce BREEDPLAN EBVs for temperament related traits based on this information.

Docility EBVs are expressed as differences in the percentage of progeny that will be scored with acceptable temperament (ie. either “docile” or “restless”). Higher, more positive, Docility EBVs are more favourable. For example, a bull with an EBV of +20 would be expected to on average produce 15% more progeny with acceptable temperament than a bull with an EBV of -10.

Flight Time EBVs are expressed as differences in the number of seconds taken for an animal to travel approximately 2.0 metres after leaving the crush. Higher (ie. longer or slower) Flight Time EBVs are more favourable. That is, higher EBVs

indicate a longer time taken to exit the crush and hence better temperament. For example, a bull with an EBV of +0.40 would be expected to on average produce progeny that took 0.25 of a second longer to exit the crush than a bull with an EBV of -0.10.

Calculation of EBVs for temperament has several major advantages over simply selecting animals based on their docility score or flight time measurement.

n Like all production traits of economic importance, the observed temperament of an animal is a combination of the genetics inherited from the sire and dam, and the environment and management under which the animal has been run. While it should not be overlooked, selection of animals simply based on their own observed temperament may have limited value in identifying animals with the most superior genetics for temperament due to the influence of the environment and/or management factors.

n EBVs for temperament related traits (as with other traits) focus on the genetic differences between animals for temperament by accounting for any environment and management influences.

n EBVs for temperament take into consideration not only the temperament of the individual animal, but also the temperament of all the animal’s relatives. In this manner, the EBVs provide a better indication of an animal’s genetics for temperament than an assessment of the animal’s temperament alone.

n EBVs allow for genetic differences in temperament to be identified between animals who themselves may have acceptable temperament. Animals who may have acceptable temperament but are likely to produce a high percentage of progeny with poor temperament can be removed from the breeding herd, or conversely, if two animals of similar genetic merit for other traits are being considered for use within a breeding program, the animal that is likely to produce a higher percentage of progeny with superior temperament can be selected.

Table 1- Breeds with Temperament Related EBVs (May 2014)

Angus Trial Docility EBVBrahman Trial Flight Time EBVHereford Trial Docility EBVLimousin Docility EBVSimmental Trial Docility EBVSanta Gertrudis Flight Time EBV

* The “Trial” status on the Docility or Flight Time EBV indicatesthat the EBV should be considered preliminary and may change as

further data is submitted by breeders. This advises that breedersare also encouraged to provide feedback on the EBV to the

breed society or BREEDPLAN

Specialised equipment is required to record flight time measurements

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Improving Genetics for TemperamentBeef producers aiming to improve the genetics of their herd for temperament can achieve this using several different selection strategies.

Culling for Poor Temperament - It is common practice for beef breeding enterprises to cull animals from the breeding herd that show unacceptable temperament. Any or all of the methods of assessing temperament listed in this article can assist with this.

Selection for Improved Temperament - Selecting animals that have superior genetics for temperament is paramount to genetically improving this trait in a beef breeding enterprise. Like other production traits, it is also important to select animals for breeding this year that are genetically superior to those used last year. This is particularly important when selecting sires due to the overall influence of their genetics in

a herd both short term and long term through daughters if retained.

The most effective information for selecting animals with superior genetics for temperament is the Estimated Breeding Value (EBV) for Docility or Flight Time. If EBVs are not available then selection using the raw docility scores or flight time records should be considered. This is with the knowledge that they will have limited scope to drive genetic progress for temperament in comparison to selection with an EBV.

Who do I contact for further information?

For further advice on the genetic improvement of temperament including recording docility scores or flight time information for the calculation of Docility EBVs or Flight Time EBVs contact staff at Southern Beef Technology Services (SBTS) or Tropical Beef Technology Services (TBTS).

T he BullSELECT workshop package has proven popular since its launch in early 2014 with 11 workshops already delivered across Australia and New Zealand.

The BullSELECT workshop package educates beef breeders about how to use the available tools to select the best bull for their enterprise. Workshop sessions include a mix of interactive discussions and presentations covering topics such as understanding the value of genetics, interpreting BREEDPLAN EBVs and using online searches including a smartphone or tablet app to source the right genetics.

Any individual seedstock breeder, groups of seedstock breeders, private consultants or State departments of Agriculture interested in hosting a BullSELECT workshop can contact staff at SBTS or TBTS to register their expression of interest. Further information, including a workshop program, is available from either the SBTS (http://sbts.une.edu.au) or TBTS website (http://tbts.une.edu.au).

BullSELECT WorkshopsProve Popular

Participants discussing bull selection at the Wirruna Poll Hereford BullSELECT workshop at Holbrook, NSW during February 2014

Participants complete a bull selection exercise at the Yancowinna Angus BullSELECT workshop at Cape Paterson, Victoria in March 2014

Continued from pg 5 - Genetic Improvement of Temperament

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percentile bands are listed across the horizontal access, with the 50th percentile being the median (or middle) value.The EBV Percentile graph provides a pictorial

representation of the percentile band in which an animal’s EBVs are ranked for each particular trait.

Percentile bands enable you to assess exactly how the current estimate of the animal’s breeding value for each trait ranks compared to the genetics of other animals that have been evaluated within the same genetic evaluation, usually being animals of the same breed.

An animal’s percentile band rank for a particular trait provides the percentage of two year old animals within the genetic evaluation whose EBV is higher than or equal to the animal’s EBV. For example, a percentile band rank of ‘top 20%’ for 400 Day Weight would indicate that 20% of two year old animals within the genetic evaluation have a 400 Day Weight EBV that is equal to or higher than the individual animal. Or put another way, 80% of two year old animals within the genetic evaluation have a 400 Day Weight EBV that is lower than the individual animal’s EBV.

The EBV Percentile graph displays a separate bar for each individual trait, with the trait listed on the vertical axis. The direction of the trait, or trait descriptor, is also provided as a reference to which direction EBVs have been ranked in the percentile bands. Generally the more favourable direction for the trait is placed on the right hand side of the graph. The

Understanding the EBVPercentile Graph

In the example EBV Percentile graph above, the animal’s EBVs would be ranked in approximately the top 25th percentile for 400 and 600 Day Weight and in the top 95th (or bottom 5th) percentile for Milk.

The EBV Percentile graph for animals can be accessed from within the EBV Enquiry facility on Internet Solutions. To access the graph, click on the bar graph icon in the top left hand corner of the animal’s EBV table, as shown below.

The BREEDPLAN website now features a “Getting Started with BREEDPLAN” area, created specifically for herds that are either new to BREEDPLAN or

potential BREEDPLAN members. This features the newly compiled “BREEDPLAN : A Guide to Getting Started” booklet, a comprehensive guide for herds enrolling with BREEDPLAN, as well as BREEDPLAN enrolment forms, BREEDPLAN fee schedules and a range of technical resources.

To access the “Getting Started with BREEDPLAN” webpage, visit the BREEDPLAN website (http://breedplan.une.edu.au) and click on the link displayed on the homepage.

“Getting Started with BREEDPLAN” Area Now Available

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Amajor research project within the Cooperative Research Centre for Beef Genetic Technologies (Beef CRC) studied ways to define the genetic control of

traditional and novel measures of reproductive performance in Tropical cattle in Northern Australia. One of the major project aims was to estimate the genetic association of young bulls’ reproductive traits with female reproduction and to identify the male genetic indicator traits that can be used to increase the rate of improvement in female reproduction in Northern Australia.

Project Design A total of 4063 male progeny were generated by natural mating between the years 2004-2010 from cows involved in the Beef CRC Lifetime Fertility Project. These were comprised of 1629 Brahmans and 2124 Tropical Composites. A total of 136 sires were used to generate the progeny, comprised of 60 Brahmans and 76 Tropical Composites. Of these, 40 sires, 13 Brahmans and 27 Tropical Composites, were used in multiple years and locations to generate genetic linkage.

Using Male Reproduction Traits to Improve Female Reproduction in Tropical Cattle

The male progeny were bred and run till weaning on research stations at “Brian Pastures” Gayndah, “Toorak” Julia Creek, “Brigalow Theodore”, “Swan’s Lagoon” Ayr and “Belmont” Rockhampton. After weaning the male progeny were transported and run at 2 locations being “Brigalow” (progeny from “Brian Pastures”, “Toorak”, “Brigalow” and “Swans Lagoon”) and “Belmont” (progeny from “Belmont”). A small number of male calves from Belmont were sent to Brigalow to maintain linkage.

The bulls were recorded pre-weaning (4 months), at weaning (6 months), and then every 3 months through to 2 years of age for a range of reproductive traits. The measurements that were recorded are outlined in Tables 1 and 2 (see next page)

Reproductive trait measurements included scrotal circumference, bull breeding soundness evaluation (BBSE), sperm morphology assessment at 12, 18 and 24 months of age and analysis of blood hormones levels for Luteinising hormone (influences testosterone production and onset of puberty), Inhibin (influences the regulation of sperm production), and Insulin-like growth factor-1 (IGF-1).

In addition, male progeny were measured for a comprehensive range of other production traits such as live weight, flight time, fatness, eye muscle area (EMA) and hip height.

ResultsYoung bulls and heifer pubertyThe research showed that the genetic correlation between male semen quality traits, mass activity, motility and percent normal sperm (PNS), and scrotal circumference were generally moderately correlated and consistent in the direction of their relationship with heifer puberty traits in both Brahmans and Tropical Composites. The genetic correlation between male hormone traits and heifer age of puberty were low with the exception of IGF-1 in Brahmans

Young bulls and female reproduction at mating 1and mating 2

Genetic correlations between male reproductive traits and female reproduction at mating 1 were generally low to moderate for both Brahmans and Tropical Composites

Male reproductive traits are useful indicators offemale reproduction in Tropical cattle.

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followed a similar pattern observed to their relationship with

heifer age at puberty.

Genetic correlations between male reproductive and female

traits at mating 2 were low for the male hormone traits, while

semen quality traits in both Brahmans and Tropical Composites

showed consistent correlations with mating 2 female traits when measured on male progeny at 18 and 24 months of age. Scrotal circumference was moderately correlated with mating 2 female traits when measured at 18 months of age in Brahman but had a low correlation with no consistent trend in Tropical Composites.

Young bulls and lifetime female reproduction

Genetic correlations between male semen quality traits, mass activity and motility, were highly correlated with lifetime female reproduction when measured at 18 months of age. Scrotal circumference showed no consistent relationship with lifetime female reproduction.

Genetic correlations between male reproductive traits and lifetime female reproduction were generally low for male hormone traits.

The results also showed that bulls with a larger protruding prepuce were genetically related to female with lower reproduction performance.

Conclusions

The results illustrate that substantial opportunity exists to improve female fertility in tropical beef cattle breeds by recording and selecting on early-in-life bull reproduction traits.

Scrotal circumference at younger ages is a modest genetic predictor of heifer age of puberty but not on lifetime female reproduction.

Semen quality such as motility, mass activity and percent normal sperm, sheath traits and some male hormone levels, were highly correlated with female reproduction, particularly with the post partum anoestrus traits in first lactation females. These traits are consequently useful as indirect selection criteria for improving female reproduction in Tropical cattle.

Opportunities exist to improve lifetime weaning rates by using bulls that have some information on the fertility of the dams from which they were derived. Preferably, these bulls should have an EBV for Days to Calving (DTC) and at the minimum, a history of their female relatives’ previous calving outcomes.

Replacement bulls should be measured and selected based on favourable Scrotal Circumference EBVs and favourable results in BBSE for semen traits such as motility, mass activity and percent normal sperm. It would also be advantageous to select bulls with good temperament and good sheath score.

Further information is available from Paul Williams at TBTS in Rockhampton on (07) 4927 6066 or paul@tbts.une.edu.au.

Table 1- Reproductive Trait MeasurementsCollected at Each Different Age

Age Weight Scrotal Blood BBSE (Mths) Sample 0 3 4 3 3 6 3 3 3 9 3 3 12 3 3 3 3 15 3 3 18 3 3 3 3 21 3 3 24 3 3 3 3

Table 2 - Measurements Collected Within Bull Breeding Soundness Evaluation (BBSE)

Physical Reproductive Semen SpermScores Check Evaluation Assessment

Leg Scrotal Mass MorphologyStructure Circumference Activity

Feet Testis Tone Motility Percent Normal Sperm

Eyes Sheath Percent Abnormal Sperm

Body PenisCondition

Table 3 - Genetic Correlation Between KeyBull & Female Reproduction Traits

BuLL TRAiTS FEMALE TRAiTS Age of Puberty Post Partum Lifetime Female Anoestrus ReproductionBRAhMANiGF-1 (6) -0.56 (0.11) -0.21(0.15) 0.20 (0.19)Scrotal (18) -0.27 (0.10) -0.27 (0.13) 0.12 (0.17)CircumferenceMass Activity (18) -0.51 (0.17) -0.27 (0.18) 0.54 (0.26)Motility% (18) -0.49 (0.20) -0.37 (0.22) 0.51 (0.28)Percent -0.48 (0.21) -0.52 (0.31) -0.01 (0.31)Normal Sperm (18)

TRoPiCAL CoMPoSiTES iGF-1 (6) -0.43 (0.11) -0.10 (0.18) -0.02 (0.17)Scrotal -0.17 (0.11) 0.13 (0.16) 0.14 (0.16)Circumference (18)Mass activity (18) -0.24 (0.20) -0.68 (0.36) 0.21 (0.25)Motility% (18) -0.38 (0.18) -0.73 (0.35) 0.29 (0.24)Percent -0.24 (0.17) -0.30 (0.25) 0.41 (0.22)Normal Sperm (18)

* Age at measure included in brackets

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Accurately recording pedigree information is one of the most fundamental jobs of a beef seedstock producer. Amongst other things, accurate pedigree

information is fundamental for the maintenance of an accurate herd book by registered breed societies, it plays a crucial role in enabling the calculation of Estimated Breeding Values (EBVs) from genetic evaluation programs such as BREEDPLAN, and allows seedstock producers to meet their duty of care to provide the most accurate information as possible on their sale animals (e.g. bulls, semen or embryos).

Even with a concerted effort to record accurate pedigrees, just how accurate is the pedigree information in the average seedstock herd? Many situations can compromise the accuracy of pedigree information, including:

n In a naturally joined single sire joining mob there is always a possibility of another bull (known or unknown) mixing with the mob at some stage.

n Artificial breeding technologies can add another source of error. If the backup bull is put in soon after the AI program, there will not be a clear break in calving between the AI calves and calves sired by the backup bull.

n In multiple sire joining programs, individual sire identification is impossible without the assistance of sire verification through DNA testing.

n “Mothering up” cows and calves may be compromised by mismothering, particularly in first calf heifers.

n Human error when recording the mating details either from natural or artificial breeding programs.

DNA parentage verification offers seedstock herds with a tool for accurately determining animal parentage and reducing pedigree errors that may otherwise occur.

DNA Parentage Verification in PracticeAn interesting case study into how easily errors can occur in pedigree recording, even in a herd following best practice guidelines, was demonstrated in the Beef Information Nucleus Progeny Test Program conducted by the Australian Limousin Breeders Society. To ensure accuracy of sire information, the sires for all calves from the first joining in 2011 were checked by DNA profiling and verification. The parentage verification highlighted a number of pedigree recording errors including:

Increasing Pedigree Accuracy with DNA Parent Verification

n The wrong straw of semen was used or the sire recorded incorrectly for three calves during the AI program.

n Four calves were incorrectly assigned to the back up bull whereas they were actually sired by the AI sire.

n Human error occurred during the data entry for another three calves.

n Two calves born on the same day had clearly swapped mothers at birth.

In total, 12 of the 227 calves (5.3%) were given incorrect sires when the pedigree information was collected. Considering the Limousin Progeny Test Program was following best practice guidelines, it is probably indicative of the lower level of pedigree errors occurring across the registered cattle industry and highlights the benefit of DNA parentage verification.

How does DNA Parentage Verification Work?There are currently two types of DNA tests for parentage verification available in Australia; microsatellite testing, which has been used for a number of years and is still a highly accurate test, and Single Nucleotide Polymorphism (SNP) testing, a new

DNA testing for parent verification excludes potential parents based their DNA profile. In this simple representation based on

microsatellite testing, Sire 2 is excluded as the calf ’s parentwhile sire 1 qualifies as the parent.

11

technology which has more recently become available as an option for parentage verification.

In general, parentage verification is based upon the detection of genetically inherited markers present in a calf ’s DNA. Calves receive one chromosome from each of their parents, and so genetic markers are passed down from parent to offspring. Both microsatellite and SNP parentage verification are based on exclusion, proving that the animal is not the offspring of a sire or dam rather than proving it is. For example if a marker is present in a calf but not in the nominated parents, then the calf is excluded as an offspring of that mating. As a result no test is 100% accurate at positively identifying an animal’s parentage. However 99.9% of incorrect matings will be detected by DNA parentage analysis.

Microsatellite MarkersA microsatellite marker is a repeat of a particular base pair sequence over and over, for example CACACACA, with current tests utilising a panel of multiple microsatellites. For example, the current microsatellite test offered by the Animal Genetics Lab (AGL) at the University of Queensland generally utilises a microsatellite marker panel of up to 21 markers, including the 12 internationally standardised markers recommended by the International Society for Animal Genetics (ISAG). A further 11 markers are available where necessary to resolve difficult parentage cases (maximum of 32 markers.). Microsatellite DNA markers have been used for nearly twenty years and remain an accurate method of parentage verification. Parentage verification tests using microsatellites are currently available in Australia through two laboratories being the AGL at the University of Queensland and Zoetis Genetics.

SNP MarkersSingle Nucleotide Polymorphisms (SNPs) are markers which identify a difference in a single nucleotide base pair. As an example, the SNP parentage verification test offered by the AGL uses a panel of ~150 SNPs, including the 100 internationally standardised ISAG SNPs.

Many breed societies have or have indicated that they will be transitioning from the use of microsatellite markers to SNP markers for parentage verification in the future. The major benefit of SNP based parentage verification over microsatellites is that it is more compatible with use of DNA technology for other purposes. For example, if breeders choose to genotype their animals with a larger SNP panel for utilisation in future genetic evaluation for their breed (e.g. GeneSeek Genomic Profiler panel available through UQ AGL, including 20,000 SNP markers), the 150 SNP profile for parentage would automatically be collected, removing the need for duplicate DNA tests to be conducted.

Unfortunately, microsatellite profiles cannot be imputed or converted to a SNP profile equivalent (or vice versa), therefore animals that require parent verification via DNA, need to have the same DNA test as their parent(s). For example if the calf has a SNP profile, the sire also needs a SNP profile. If the sire only has a microsatellite profile, it needs to be re-genotyped to have a SNP profile available. Hence transitioning to SNP parentage verification can come at an additional cost to the seedstock breeder and as a result some Breed Societies have chosen to continue using microsatellite markers in the short term.

Breed Society RegulationsIn addition to the benefit of using DNA parentage verification to improve pedigree accuracy, most breed societies have registration requirements and regulations around DNA profiling and parent verification. These will include minimum DNA parentage verification requirements and which type of profile they accept (e.g. microsatellite or SNP) both now and in the future. It will also include the process to follow to submit the sample (e.g. facilitated by the breed society or direct to the laboratory). If you are not aware of the regulations for your breed, you are encouraged to contact your breed society directly for this information.

How to Get your Cattle TestedThe genotyping laboratories offering this service in Australia (e.g. Zoetis Genetics and AGL) generally use tail hair samples (hair roots attached) as a source of DNA, however they can use other samples such as blood, semen or tissue if required. Most breed societies have regulations for DNA profiling which may include the preferred use of one or both of these laboratories. They will also have a process in place for collection and submission of the DNA sample for profiling and parent

Collecting a DNA Sample for DNA parent verification,pull 20-30 thick hairs from the brush of the animal’s tail

including the hair roots.

Continued on pg 12

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verification. This may include supplying the DNA sample collection kits and facilitating the submission of the kits to the laboratory. Or the breed society may prefer that you work with your preferred laboratory directly.

General Guidelines for submitting DNA for parentage verification:

1. Contact your Breed Society or the DNA lab for a DNA sample collection kit

2. Pull 20-30 thick hairs from the brush of the animal’s tail including the hair roots.

3. Complete the required submissions forms

Continued from pg 11 - Increasing Pedigree Accuracy with DNA Parent Verification

4. Mail the forms plus the DNA sample to your breed society or the genotyping laboratory. This depends on your breed society’s arrangement with the genotyping laboratory

5. The results to be returned by email or mail. The results may also be supplied direct to you breed society. The turnaround time will depend on the laboratory and level of activity at the time of submission. As a general guide, turnaround time is 4 to 6 weeks.

Reference: UQ AGL - “DNA Parentage Testing - Fact Sheet”. Link - http://www.uq.edu.au/vetschool/content/animal-genetics-laboratory/dna-parentage-testing.pdf

Herefords Australia and the Australian Simmental Breeders Association recently became the latest breeds to publish EBVs for temperament with the

release of Trial Docility EBVs for Hereford and Simmental animals in February and March 2014 respectively.

Trial Docility EBVs are now calculated as part of the routine monthly TransTasman Hereford and Simmental BREEDPLAN analysis for animals that have either been scored for docility, or have progeny scored for docility, and are being made available in a similar fashion to other EBVs.

Trial Docility EBVs can be viewed in BREEDPLAN herd reports, on the Hereford and Simmental online animal search facility (i.e. Internet Solutions) or through herd recording programs (e.g. HerdMaster) by importing the latest GROUPEBV file.

Docility EBVs Now Available for Hereford and Simmental Animals

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Table 1- Docility Scoring Codes and Descriptions

Score Code Description

1 Docile Mild disposition, gentle and easily handled, stands and moves slowly during handling, undisturbed, settled, somewhat dull, does not pull on headgate when in crush, exits crush calmly.

2 Restless Quiet but slightly restless, may be stubborn during handling, may try to back out of crush, pulls back on headgate, some flicking of tail, exits crush promptly.

3 Nervous Manageable but nervous and impatient, a moderate amount of struggling, movement and tail flicking, repeated pushing and pulling on headgate, exits crush briskly.

4 Flighty Jumpy and out of control, quivers and struggles violently, may bellow and froth at mouth, continuous tail flicking, defecates and urinates during handling, frantically runs fenceline and may jump when penned individually, exhibits long flight distance and exits crush wildly.

5 Agressive May be similar to score 4 but with added aggressive behaviour, fearful, extreme agitation, continuous movement which may include jumping and bellowing while in crush, exits crush frantically and may exhibit attack behaviour when handled alone.

BREEDPLAN now produces Docility EBVs for animals within the Angus, Hereford, Limousin and Simmental breeds, based on the collection of docility scores.

Seedstock producers within these breeds who place importance on improved temperament within their breeding objective should consequently consider the submission of docility score information to BREEDPLAN.

Docility scores, being the subjective assessment of animals’ temperament, can be recorded on animals when the animals are between 60 and 400 days of age. Animals are usually scored at weaning or shortly afterwards, which in practise is often co-ordinated with the collection of 200 day weight information. The advantage of scoring at weaning is that all calves will have had minimal handling and so will express variation in temperament, while variation between animals in handling prior to scoring will also be minimised.

Either a yard test can be used where calves are individually put into a small square yard and the handler attempts to hold the animal in one corner for about 30 seconds, or a crush test where calves are put up a race and held in a crush or weigh scales for about 30 seconds but not head bailed.

When using the crush or yard test, the behaviour of animals is observed and animals scored on a 1-5 scale, with 1 being ‘docile’ and 5 being ‘aggressive’. A detailed description of the different scores is included in Table 1.

When docility score information is being collected, it is important to consider:

n There needs to be some variation in the scores for them to be useful. That is, scoring all animals in a group with a docility score of [1] will not identify any genetic differences in docility.

Recording Docility Scores for BREEDPLAN

n BREEDPLAN can accept half scores if animals exhibit behaviour which is intermediate to the above scores.

n Animals should be assigned a different “temperament management group” if they have had a different level of handling prior to scoring.

n The method of scoring used (ie. crush or yard) should be specified when submitting the docility scores to BREEDPLAN.

n When recording docility scores, it is important that both a consistent scoring method is used and the same person scores all animals that are being assessed in the herd on that particular day.

Docility scores should be submitted directly to the BREEDPLAN office at ABRI, with updated Docility EBVs becoming available at each routine monthly GROUP BREEDPLAN analysis.

While Docility EBVs are currently only published for Angus, Hereford, Limousin and Simmental animals, several other breeds have also indicated a desire to publish Docility EBVs once sufficient docility score information has been collected.

Seedstock producers from other breeds are consequently encouraged to consider the collection of docility score information.

Comprehensive docility score information has now beencollected on Limousin animals

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Anumber of significant enhancements were applied to the BREEDPLAN software that is used to calculate EBVs for Hereford animals within the February 2013

TransTasman Hereford GROUP BREEDPLAN analysis. These enhancements have resulted in the calculation of improved BREEDPLAN EBVs for Hereford animals and are part of the normal evolution of the BREEDPLAN software.

The enhancements include:

Upgrade to BREEDPLAN Version 6.2This latest version of BREEDPLAN software has several enhancements over the software previously used within the TransTasman Hereford BREEDPLAN analysis including a revised method for calculating accuracy values for Days to Calving EBVs, a revised method for handling different groups of “base” animals, and the ability to “blend” genomic prediction information (ie. DNA information) into the analysis when genomic predictions relevant to Australian and New Zealand Hereford animals become available.

Introduction of a Trial Docility EBVFollowing the collection of docility scores on over 7,000 Hereford animals, a “trial” Docility EBV has been published for animals within the TransTasman BREEDPLAN evaluation. Further information is included on page 12.

Revised Selection IndexesThe parameters used to calculate the Supermarket, Grass Fed Steer, Grain Fed Steer and EU selection indexes for Australian Hereford animals has been updated following a review of the previous indexes by members of the Herefords Australia Technical Committee. The most notable changes include:

n the economic and production parameters within all selection indexes have been updated

n increased emphasis has been placed on improved eating quality and tenderness in all selection indexes to favour animals that are suited to producing progeny that meet MSA requirements

n modification has been made to the Grain Fed Steer index to make it suitable for use by producers conducting black baldy crossbreeding programs where Hereford bulls are being used over an Angus based cow herd (in addition to use

Enhancements Made to Hereford GROUP BREEDPLAN

by producers conducting straight bred Hereford programs and targeting high quality, highly marbled markets)

n modification has been made to the Grass Fed Steer index to make it suitable for use by producers using Hereford bulls over a Bos indicus based cow herd (in addition to use by producers conducting straight bred Hereford programs and targeting the production of heavy steers off grass)

n modification has been made to the EU index to reflect both grass and grain fed finishing production systems

Further information regarding the Supermarket, Grass Fed Steer, Grain Fed Steer and EU selection indexes that are now calculated for Australian Hereford animals is available from the BREEDPLAN website.

If you have any questions regarding the enhancements to Hereford BREEDPLAN, please contact staff at Southern Beef Technology Services on (02) 6773 3555 or via email office@sbts.une.edu.au.

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@SBTSTBTS SBTS & TBTS sbtstbts

Follow SBTS & TBTS on Social Media

Beef producers can keep up to date with the latest developments in genetic technologies and the activities of SBTS and TBTS by following SBTS and TBTS on

Facebook, Twitter and YouTube. Information is routinely posted on Twitter and Facebook such as articles, webinars and event details, while the YouTube channel contains video presentations such as webinars from past webinar series and short “Understanding BREEDPLAN EBVs” video clips.

To follow SBTS and TBTS on Twitter, Facebook or YouTube simply go to the SBTS or TBTS website and click on the

relevant icon, or go directly to the SBTS & TBTS Facebook account at http://facebook.com/SBTSTBTS, Twitter account at http://twitter.com/SBTSTBTS or YouTube Channel at http://youtube.com/user/sbtstbts.

Staff Departures - Christian Duff and Andrew Byrne

The SBTS & TBTS teams bidded farewell to Christian Duff and Andrew Byrne during June 2014 with both resigning from their current positions to pursue other

career opportunities within the beef seedstock industry.

Christian and Andrew will be replaced by Alex McDonald as the Technical Officer allocated to provide technical support services to Charolais, Hereford, Red Angus, Shorthorn, Simmental and Wagyu seedstock producers regarding the application of genetic technologies.

Alex has been closely associated with the SBTS team since the inception of the SBTS project in 2005 during which time he has performed an important role as a senior consultant. Alex has had a long career within the beef industry having been

employed as the General Manager of the Australian Limousin Breeders Society since 1992 but stepped down from this position on 30 June.

The SBTS & TBTS teams would like to thank both Christian and Andrew for their contribution over the past 12 and 9 years respectively and wish them both the very best with their future endeavours.

Staff Movements - Gemma WilkinsonNow Based in Southern NSW

Technical officer within the SBTS project, Gemma Wilkinson, has recently relocated from the ABRI office in Armidale and is now based in Young, NSW.

Gemma has retained all her existing responsibilities within the SBTS & TBTS projects, including the provision of technical support to members of the Murray Grey, South Devon, Gelbvieh, Devon, Red Poll, Blonde d’ Aquitaine and Salers breeds.

Gemma can be contacted by phone on 0459 823 067 or email gemma@sbts.une.edu.au.

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Southern Beef Technology ServicesTelephone: (02) 6773 3555Email: office@sbts.une.edu.auWeb: http://sbts.une.edu.au

Tropical Beef Technology ServicesTelephone: (07) 4927 6066Email: office@tbts.une.edu.auWeb: http://tbts.une.edu.au

If you would like any further information on SBTS and TBTS please contact:

Charolais Red Angus Shorthorn Simmental Wagyu

hereford

Belmont Red Droughtmaster Brahman Santa Gertrudis Brangus Senepol Charbray Simbrah

Blonde d’Aquitaine Red Poll Devon Salers Gelbvieh South Devon Murray Grey

Limousin

Angus

Accessing Support in Application ofGenetic Technologies

For support and assistance in the use and understanding of the different genetic technologies that are available, such as BREEDPLAN, BreedObject Selection Indexes, Internet Solutions, TakeStock, GeneProb, Mate Selection Software & DNA based tools or to discuss any of the information included in this edition of the SBTS & TBTS Update, please contact:

Alex McDonald

Alex McDonald

Paul Williams

Gemma Wilkinson

Alex McDonald

PeterParnell

alex@sbts.une.edu.au(02) 6773 2472

alex@sbts.une.edu.au(02) 6773 2472

paul@tbts.une.edu.au(07) 4927 6066

gemma@sbts.une.edu.au(02) 6773 3265

alex@sbts.une.edu.au(02) 6773 2472

peter@angusaustralia.com.au(02) 6772 3011

Technical Consultant Breeds Contact Details