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Comparative and Functional GenomicsComp Funct Genom 2005; 6: 174–180.Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.467

Conference Paper

Conference review: bovine genomics fromacademia to industryCattle and Sheep Workshop, Plant & Animal Genomes (PAG) XIIIConference, San Diego, CA, USA

David Henderson1*, Milt Thomas2 and Yang Da3

1Department of Animal Sciences, The University of Arizona, Tucson, AZ 85721, USA2Department of Animal and Range Sciences, New Mexico State University, Las Cruces, NM 88003, USA3Department of Animals Sciences, University of Minnesota, St. Paul, MN 55108-6118, USA

*Correspondence to:David Henderson, 231 ShantzBuilding, Department of AnimalSciences, The University ofArizona, Tucson, AZ85721, USA.E-mail:[email protected]

Received: 31 January 2005Accepted: 2 February 2005

Introduction

Two multistate United States Agricultural Exper-iment Station projects, North Central (NC)-1010and National Research Support Project (NRSP)-8,collaborated on a joint presentation at the PAGXIIIconference in San Diego, CA. The joint sessionconsisted of presentations on current and futuretechnologies for ruminant research. Topics rangedfrom genome discovery to tool applications. Thecurrent state of the art in bovine and ovine researchis near that seen in the model organisms, althoughresearch methods may be a few steps back ofmany near future technologies that researchers ofmodel organisms are currently developing (see thesection on Trey Ideker for an example). Currentproblems that need immediate attention are thoseof implementation of research findings and edu-cation of producers as to how they might imple-ment the results of quantitative trait loci (QTL)scans and candidate gene searches. The outcomesof the committee indicate that bioinformatics andcomputational biology approaches in both tool

development and tool usage will be major areasof emphasis for the next few years. The follow-ing review will highlight information that was pre-sented in the areas of genetic markers, gene map-ping and sequencing, bioinformatics, functionalgenomics, as well as industry perspectives. Sum-maries of the NC-1010 and NRSP-8 committeeswill also be presented.

Bovine sequencing efforts

Jim Womack from Texas A&M University gavea detailed presentation entitled ‘Highlights of thebovine sequencing project’. The sequence of thehuman genome was published in 2001 [23] andthis publication necessitated sequencing of a bovinegenome for both agricultural purposes and for useof the bovine as a model organism to study humanhealth. The following organizations contributed tothe project:

• National Human Genome Research Institute($25 million).

Copyright 2005 John Wiley & Sons, Ltd.

Bovine genomics — academia to industry 175

• USDA-National Research Inititiative ($10million).

• State of Texas ($8 million).• Genome Canada ($5 million).• Kleberg Association ($2 million).• USDA-ARS ($1 million).• CSIRO Australia ($1 million).• New Zealand ($1 million).• United States Beef Council ($0.4 million).• Texas Beef Council and South Dakota Beef

Council (<$0.2 million).

Jim Womack reviewed the discussions towardssequencing a bovine genome, which were startedas early as 1993 by the cattle and sheep discus-sion group known as NRSP-8. This project, whichis known as the International Bovine GenomeSequencing Project, was initiated in 2003 and isdirected by a steering committee. Much of the ini-tial sequencing effort is occurring at the HumanGenome Sequencing Center at Baylor College ofMedicine in Houston, TX. Richard Gibbs andGeorge Weinstock are directing these efforts anda ∼3× working draft was published in Octo-ber of 2004 and is available at GenBank. Theanimal resources from this project were derivedfrom the historic linebreeding Hereford projectat the Fort Keogh US Department of Agricul-ture–Agriculture Research Service (USDA-ARS)station in Miles City, Montana [12,13,19]. A bac-terial artificial chromosome (BAC) DNA librarywas originally created from tissues of the bull L1Domino 99 375, and the whole genome shotgunsequences were derived from DNA extracted fromthe white blood cells of his daughter, L1 Dominette01 449. Dominette was selected since her sire wasused to create the BAC library and because ofthe concept that sequence assembly could be madeeasier working with sequences from animals withsimilarities in their genetic background. Other con-tributions to this project now include sequencingwithin other breeds such as Holstein, Angus, Brah-man, Jersey, Limousine and Norway Red. Some ofthese other efforts include SNP mapping, as wellas ∼10 000 full-length mRNA sequences to be pro-vided by Genome Canada. A 7–8× coverage mapis expected by late summer of 2005.

Bioinformatics

Trey Ideker of the University of California, SanDiego, gave a presentation entitled ‘Modeling cells

with molecular interaction networks’. Molecularinteraction networks are experimentally derivedconnections of metabolites and proteins withinpathways. While these molecules may not directlyinteract, they likely are related through the enzymesthat process them. Dr Ideker presented evidencethat overlays, the alignment of pathways accord-ing to protein sequence or other data where sim-ilarity scores are available, may be of great use.Specifically, overlays of known networks fromwell-studied species may elucidate the function orrole of unknown metabolites and proteins in lesswell understood organisms. The implications of thisresearch involve an increase in the speed of whichfunction can be ascribed to unknown compoundsin bovine, using information gathered in human,mouse and rat.

Christian Looft of the University of Kiel, Ger-many, presented material on the ‘Structural andfunctional analysis of antimicrobial peptides inthe bovine mammary gland’. Dr Looft was inter-ested in the expression of β-defensin genes withinthe bovine mammary gland. Following a genomiccharacterization of defensin genes, seven novel β-defensin genes and four pseudo-genes were identi-fied and mapped in two BAC contigs that spannedapproximately 700 kb. Another antimicrobial pep-tide, psoriasin, was investigated based upon thefunctionality of the human homologue for anti-E. coli activity. The peptide was isolated frombovine dander and characterized by MS. In anironic twist of fate, an E. coli was used to replicatea recombinant version of the peptide. The groupwas able to demonstrate the anti- E. coli activityof this peptide when presented outside of the cellmembrane, while showing that the peptide is notable to kill E. coli cells while still inside the cellmembrane.

Christine Elsik of Texas A&M University(TAMU) spoke on the current state of the bovinelong oligo array developed among a consortiumof researchers at TAMU, University of Missouri,Iowa State University, and The University of Min-nesota. Sequences mined from GenBank are cur-rently undergoing a screening process to removeduplicated sequences, vector sequences and otherartifacts of the cloning process. It is expectedthat a first draft of the sequences to be spot-ted on the array will be available by Summer2005.

Copyright 2005 John Wiley & Sons, Ltd. Comp Funct Genom 2005; 6: 174–180.

176 D. Henderson, M. Thomas and Y. Da

Functional genomics

Mark Jutila (Montana State University) presentedresults of functional genomics analysis of bovinegammadelta and αβ T cells from USDA-Initiativefor Future Agriculture and Food Systems (IFAFS)-and National Institutes of Health (NIH)-fundedprojects in collaboration with Mitchell Abraham-sen (University of Minnesota) [7,8,14]. Changesin bovine γ δ and αβ T cells in the draining lym-phatics of the gut mucosa following S. typhimuriuminfection were determined by fluorescent activatedcell sorting (FACS) and microarray analyses. Can-nulae were inserted into the mesenteric lymphaticducts of calves for collection of cells draining fromthe intestine and lymphatic fluid collected at inter-vals pre- and post-infection. In the blood of calveswith a fever and diarrhoea, neutrophils, monocytesand B cells increased slightly during the courseof the 72 h infection, whereas in the lymphaticfluid, γ δ T cells steadily increased in frequencyand all other cell types decreased or remained con-stant. During two such procedures, the γ δ andαβ T cells were purified in sufficient numbersfor RNA isolation and genomic analysis. BovinecDNA (Pyxis Cattle 7600) and Affymetrix bovineoligonucleotide arrays were utilized to elucidatethe changes in gene expression at 0, 6 and 24 hafter S. typhimurium infection in both T cell sub-sets. The magnitude of the response in both T celltypes was comparable, but the genes that changedwere different. The Affymetrix arrays allowed forcomparison over the time course within one sub-set, as well as comparison between cell types,and revealed more than 1000 genes differentiallyexpressed between γ δ and αβ T cells at 0 and6 h post-infection. Affymetrix arrays also demon-strated the expression of known immune relatedgenes suggesting distinct functions of the T cellsubsets during early S. typhimurium infection.

Animal traceability, gene and QTLmapping

Michael Heaton of the USDA-ARS Meat AnimalResearch Center (MARC) presented material on‘bovine single nucleotide polymorphisms (SNP)s:animal identification, traceback and pedigree verifi-cation’ in the NC1010 symposium. Parent verifica-tion and the ability to trace animal products using

DNA polymorphism procedures are now being uti-lized by the livestock industries. Microsatelliteswere the original technology for these procedures;however, usable SNPs have now been published[6], with another publication in press in the Jour-nal of the American Veterinary Medical Associa-tion soon to assist these findings. These proce-dures proved valuable when bovine spongiformencephalopathy (BSE) was detected in the USA inDecember 2003. A team of scientists representingthe USDA-ARS and two commercial genotypinglabs developed assays so that in a time span of48–72 h, field veterinarians and staff of USDA-Animal Plant Health Inspection Service (APHIS)could trace meat products from slaughter facilityto farm.

Stephen White from USDA-ARS MARC pre-sented a talk on ‘New SNP marker in CAPN-1associated with tenderness in cattle of indicine, tau-rine and admixed descent’. There is tremendousinterest in the trait of tenderness in the basic scien-tific community and in the commercial genotypingindustry. A challenge in the application of someof the initially discovered polymorphisms relatedto tenderness was that the markers inferred vari-ability in prediction of tenderness traits and haddiversity among genotypes in Bos taurus cattle, butnot in Bos indicus cattle [3,17,18]. These studiesrevealed that chromosome 29 contained an impor-tant gene defined as µ-calpain (CAPN-1), whichhas a large role in post-mortem tenderization. Thereare a series of SNPs within or closely linked to thisgene. Two of these SNPs appear to be informa-tive in Bos indicus and Bos taurus cattle (316 and4753), but a SNP at 530 only appears to be infor-mative in Bos taurus cattle. Moreover, it appearsthat these markers maybe more useful in predic-tions using analytical procedures involving haplo-types.

Stephen Moore from the University of Albertaat Edmonton delivered a talk on ‘Candidate genesof feed efficiency’. The trait of residual feed intakewas introduced [9] and efforts to find genetic toolsto select for this trait were discussed. Data on othermeasures of animal efficiency, which involvedevaluating oxygen consumption and methane pro-duction using a respiratory calorimetry hood, werealso presented. The rationale for these measurescomes from the concept that measures of gasconsumption or production could be used to esti-mate metabolic rate/efficiency in cattle. Efforts to



use these measures to identify candidate genes werealso presented, particularly their associations withhormones such as leptin [16].

Jeremy Taylor (University of Missouri) reportedresults in fine quantitative trait loci (QTL) map-ping in dairy cattle (in collaboration with scientistsat USDA-ARS and the University of Arizona), aswell as results in positional cloning in beef cattle.To fine-map QTL affecting milk production traitsin dairy cattle on BTA6 [1], 3317 bulls comprising45 half-sib families were genotyped for 38 mark-ers. The data were analysed using least squaresregression (QTL Express), linkage disequilibrium(LDVCM) and full pedigree MCMC (LOKI) meth-ods. A total of 19 sires were segregating for at leastone QTL under a half-sib model at chromosome-wide p < 0.05. LD results across families indi-cated the presence of up to seven QTLs (threewithin a 6 cM region), whereas LOKI revealedonly three QTLs. Positional/functional candidategenes have been identified for five of the QTLs.Osteopontin (OPN or SPP1) is a strong candidatefor the QTL near marker BM143. The entire OPNgene and 5 kb upstream was sequenced from foursegregating sires and four non-segregating sires(12.3 kb/animal). A total of 15 SNPs were iden-tified but only one SNP resulted in sire geno-types that were concordant with the segregationstatus of all eight sires. For position cloning inbeef cattle, the strategy outlined in Taylor andSchnabel [20] was applied and built upon the pre-vious projects involving Bos taurus × Bos indi-cus crosses [10] and study of Bos taurus autoso-mal (BTA) chromosomes 2 and 14 [5,11,15]. ADNA repository from the semen of 1660 registeredbulls representing 14 generations of the Ameri-can Angus Association was assembled. Expectedprogeny differences (EPDs) and reliabilities for 20traits are available for this population. In addi-tion, 5300 DNA samples were collected on com-mercial Angus steers (36 half-sib families haveat least 30 progeny) with growth and slaughterphenotypes. A total of 113 637 genotypes for 56microsatellite loci and SNPs for thyroglobulin inexon 5 (TG5) and diacyl glycerol acyltransferasein exon 1 (DGAT1) on BTA2 and BTA14 in 1361Angus sires and 559 steers were scored. The geno-prob program of Thallman et al. [21,22] assistedin the pedigree analyses. The results suggested thatTG5 had no effect on sire marbling EPDs or steermarbling phenotypes. Three previously published

marbling QTLs, one birth weight QTL and onecarcass weight QTL are segregating within Angusand map to identical locations to the publishedreports.

Industry perspective

John Pollack from Cornell University spoke onNBCEC efforts in marker validation. The NationalBeef Cattle Evaluation Consortium (NBCEC) isa consortium of four universities involved ingenetic evaluation of beef cattle breeds. Col-orado State, Cornell, Iowa State and Georgiaare the participating universities. The consor-tium is supported by a federally funded spe-cial grant and part of the funds from that grantare used to support educational programs (http://www.ansci.cornell.edu/nbcec/index.html). Be-cause of the role of the consortium in nationalcattle evaluation and recent introduction of marker-assisted EPDs (http://www.simmental.org/ASA Today/Cow%20Awards%20Folders/MAEPDs.html), NBCEC has formed a QTL teamto develop procedures for validating commercial-ized genetic markers. Members of the QTL teamare R. L. Quass of Cornell University, R. M. Thall-man of USDA-ARS-MARC, and R. L. Fernando ofIowa State University. In general, the consortiumwill conduct blind testing of markers in resourcepopulations. The current test populations involveDNA and data from the National Cattlemen’s BeefAssociation (NCBA) Carcass Merit Project, out-reach projects of NBCEC involving the Bell andKing ranches, and cycles 7 and 8 of the USDA-ARS Germplasm Evaluation Program [4]. The con-sortium is seeking samples and data from otherresearch and resource populations, as they wouldlike to develop a repository with ample repre-sentation of British, Continental and Bos indicus-influenced breeds. Dr Pollock stated that ‘there arethree challenges currently facing the beef cattleindustry with the use of genetic marker informa-tion for genetic improvement programs: (a) DNAmarker information is not being adequately col-lected by breed associations; (b) there are no polic-ing mechanisms for use and interpretation of DNAmarker information; and (c) assessment of markersis not currently part of the process of evaluation ofDNA markers.


http://www.ansci.cornell.edu/nbcec/index.html

http://www.simmental.org/ASA_Today/Cow%20Awards%20Folders/MAEPDs.html

http://www.ansci.cornell.edu/nbcec/index.html




Michael Cowan (Accelerated Genetics) dis-cussed his company’s practice and results of apply-ing marker-assisted selection in dairy cattle. Hiscompany started applying marker techniques togenetic selection in 1988 by screening impact sirefamilies, using polymorphisms in known genes,with the goal of improving the accuracy in select-ing young bulls prior to entering progeny-testingprograms [2]. Restriction fragment length poly-morphisms (RFLP) in the prolactin/placental lac-togen gene family and gene markers involved inimmunity and lactation (DRB and CYP21) haplo-types were screened for three sire families for theireffects on the predicted transmitting ability (PTA)of milk, fat and protein yields, as well as compositeyields measured by dollars, and found significantmarker effects. Full sib comparisons showed sig-nificant improvement in the realized gains in theabove traits. The company also used genetic mark-ers to monitor semen processing, parentage iden-tification and inheritance of new genetic defects.To improve the efficiency of marker-assisted selec-tion in the dairy industry, more work is needed inthe following areas: characterization of additionalbovine clones and regulatory sequences, develop-ment of methods to rapidly screen genomes ofmultiple individuals, better understanding of genefunction and interactions, and more emphasis ontraits with low heritabilities.

Marjorie Faust from ABS Global Inc., spoke on‘How do we move from the laboratory to the bullbarn?’ QTL mapping efforts have delivered manypromising candidate genes for selection within theHolstein breed, or other bovine breeds in gen-eral. There is little consistency in how these genesare utilized, or characterized within commercialpopulations. The producer often lacks the techni-cal expertise to master the nuances of effect andefficacy of each candidate gene commonly under-stood by the scientific community. Better effortsto appropriately educate the producer and to eval-uate potential gene targets for selection in rele-vant populations are necessary for marker-assistedselection to succeed as a commonly used commer-cial tool. It also appears that the cost of imple-menting marker-assisted selection is the role of thesemen stud rather than the organization wantingto benefit from the new selection tool. The indus-try currently would like to pay less per unit ofsemen, which results in limited dollars for the costof genotyping.

Summary of NSRP-8 station report:cattle, sheep and goats

The objectives of this project NSRP-8 are:

1. Enhance and integrate genetic and physicalmaps of agriculturally important animals forcross-species comparisons and sequence anno-tation.

2. Facilitate integration of genomic, transcrip-tional, proteomic and metabolomic approachestoward better understanding of biological mech-anisms underlying economically important tra-its.

3. Facilitate and implement bioinformatics tools toextract, analyse, store and disseminate informa-tion.

Scientists from the University of Arkansas, theUniversity of California at Davis, the Univer-sity of Illinois, Iowa State University, LouisianaState University, Purdue University, New MexicoState University, Oklahoma State University, TexasA&M University, Utah State University, the Uni-versity of Wisconsin–Madison and a few otheruniversities gathered to present and discuss infor-mation regarding these objectives. The scope ofthe information ranged from mapping projects anddefining QTL to presentation of the effects of poly-morphisms in candidate genes in cattle and sheepchallenged with different production systems andenvironments. Genetic influences of lactation andbehavioural traits such as disposition were also dis-cussed, as were the influences of genetic anomalies,such as callipyge. Milt Thomas of New MexicoState University served as the session coordinatorand was assisted by secretary Udaya Desilva ofOklahoma State University, who will serve as thesession coordinator in 2006. Clare Gill of TexasA&M University was elected to serve as the sec-retary in 2006. Bioinformatic information was alsopresented and the committee voted to include dis-cussion of goats into the symposium.

Summary of NC-1010 station report

The objectives of this multi-state project are:

1. Determine the location, structure, function andexpression of genes affecting health, reproduc-tion, production and product quality in cattle.



2. Interpret and apply genomics and proteomicsinformation by developing statistical/bioinfor-matics methods and utilizing molecular tools incattle.

3. Develop and deliver educational materials aboutbovine genomics research to consumers andstakeholders.

Scientists from the University of Arizona, theUniversity of California at Davis, Michigan StateUniversity, Texas A&M University, the Universityof Vermont, the University of Illinois (Urbana–Champagne), Ohio State University, the Universityof Minnesota and the University of Wisconsin wererepresented. Alison van Eenennaam of UC–Davisserved as chair of the session, assisted by secretaryDavid Henderson of the University of Arizona.Primary discussion centred on the development ofeducational material on biotechnology aimed atproducers. The chosen medium was the World-Wide-Web and it is to be hosted at UC–Davis.David Henderson will serve as chair next year andClare Gill of Texas A&M University will serve assecretary next year.

This project would like to:

1. Continue development of educational materialon biotechnology.

2. Develop material for a booth at the 2006 Amer-ican Society of Animal Scientists/AmericanDairy Science Association meeting and conducta graduate student poster session at the nextmeeting of NC-1010.

Conclusions

Biotechnology research of the bovine and ovineis lagging behind that of the basic model organ-isms only in the understanding of the organism;however, now that sequence is becoming avail-able, knowledge of these species will accelerate.QTLs for many production and quality traits areeither mapped or are being mapped and candidategenes for selection are under investigation. Futurework in the model organisms is likely to producenew tools that will help elucidate the underlyingbiology behind such complicated biological pro-cesses as feed conversion and efficiency to mar-bling and meat quality. Defining these technicaldevelopments is needed, to educate producers on

the use and importance of genomic technologies inmodern agricultural practice.

Acknowledgements

The authors would like to acknowledge the AgriculturalExperimental Stations of the University of Arizona, NewMexico State University and the University of Minnesota,and the Agricultural Experiment Station efforts in thecommittees of NC1010 (Interpreting Cattle Genomic Data:Biology, Applications and Outreach) and NRSP-8 (NationalAnimal Genome Research Program — National ResearchSupport Project 8) focused on cattle, sheep and goats.

References

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