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Food, fibre and pharmaceuticals from animals
RESEARCH FRONT

Capturing benefits from the bovine genome sequence

Ross L. Tellam

CSIRO Livestock Industries, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, Qld 4067, Australia. Email: Ross.Tellam@csiro.au

Australian Journal of Experimental Agriculture 47(9) 1039-1050 http://dx.doi.org/10.1071/EA06032
Submitted: 10 January 2006  Accepted: 6 September 2006   Published: 6 August 2007

Abstract

The bovine genome sequence in ‘draft’ form will be complete in 2007. The availability of the sequence and very large numbers of single nucleotide polymorphisms will have profound effects on livestock production. The dairy industry is well positioned to capture the benefits of this enormous and enabling resource because of its comprehensive databases containing phenotypic and pedigree data for large numbers of animals, intense utilisation of genetics in breeding programs and efficient management of reproductive performance. The bovine genome sequence will assist in the development of novel products, especially value-added products, and markedly enhance the rate of genetic gain in the Australian dairy population. The immediate challenge facing the industry is the integration of new technological capabilities into existing breeding programs and production systems.

Additional keywords: cow, ruminant.


References

Anon.  (2005) Australian dairy productions systems and profit. Available at http://www.dairyaustralia.com.au [Verified 25 May 2007]

Austin CP Battey JF Bradley A Bucan M Capecchi M et al 2004 The knockout mouse project. Nature Genetics 36 921 924 DOI

Band MR Larson JH Rebeiz M Green CA Heyen DW et al 2000 An ordered comparative map of the cattle and human genomes. Genome Research 10 1359 1368 DOI

Band MR Olmstead C Everts RE Liu ZL Lewin HA 2002 A 3800 gene microarray for cattle functional genomics: comparison of gene expression in spleen, placenta, and brain. Animal Biotechnology 13 163 172 DOI

Banks RG 2005 Challenges with investing in genetic improvement for the Australian extensive livestock industries. Australian Journal of Experimental Agriculture 45 1033 1039 DOI

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 DOI

Barendse W Vaiman D Kemp SJ Sugimoto Y Armitage SM et al 1997 A medium-density genetic linkage map of the bovine genome. Mammalian Genome 8 21 28 DOI

Byrne KA Wang YH Lehnert SA Harper GS McWilliam SM Bruce HL Reverter A 2005 Gene expression profiling of muscle tissue in Brahman steers during nutritional restriction. Journal of Animal Science 83 1 12

Carter N 2004 As normal as normal can be? Nature Genetics 36 931 932
DOI

Charlier C Coppieters W Farnir F Grobet L Leroy PL et al 1995 The mh gene causing double-muscling in cattle maps to bovine Chromosome 2. Mammalian Genome 6 788 792 DOI

Charlier C Segers K Karim L Shay T Gyapay G Cockett N Georges M 2001 The callipyge mutation enhances the expression of coregulated imprinted genes in cis without affecting their imprinting status. Nature Genetics 27 367 369 DOI

Cheng J Kapranov P Drenkow J Dike S Brubaker S et al 2005 Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308 1149 1154 DOI

Cheung VG Spielman RS Ewens KG Weber TM Morley M Burdick JT 2005 Mapping determinants of human gene expression by regional and genome-wide association. Nature 437 1365 1369 DOI

Chitko-McKown CG Fox JM Miller LC Heaton MP Bono JL Keen JE Grosse WM Laegreid WW 2004 Gene expression profiling of bovine macrophages in response to Escherichia coli O157:H7 lipopolysaccharide. Developmental and Comparative Immunology 28 635 645 DOI

Chiu R, Bosdet I, Mathewson C, Wye N, Lee D, et al (2004) A BAC physical map of the bovine genome. PAG XII p. 623. Available at http://www.intl-pag.org/pag/12/abstracts/P5j_PAG12_623.html [Verified 25 May 2007]

Clop A Marcq F Takeda H Pirottin D Tordoir X et al 2006 A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nature Genetics 38 813 818 DOI

Cockett NE Smit MA Bidwell CA Segers K Hadfield TL Snowder GD Georges M Charlier C 2005 The callipyge mutation and other genes that affect muscle hypertrophy in sheep. Genetics, Selection, Evolution. 37 S65 S81 DOI

Cohen-Zinder M Seroussi E Larkin DM Loor JJ Everts-van der Wind A et al 2005 Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle. Genome Research 15 936 944 DOI

Collins FS Green ED Guttmacher AR Guyer MS 2003 A vision for the future of genomics research. Nature 422 835 DOI

Dalrymple BP 2005 Harnessing the bovine genome sequence for the Australian cattle and sheep industries. Australian Journal of Experimental Agriculture 45 1011 1016 DOI

Dean W Santos F Stojkovic M Zakhartchenko V Walter J Wolf E Reik W 2001 Conservation of methylation reprogramming in mammalian development: aberrant reprogramming in cloned embryos. Proceedings of the National Academy of Sciences of the United States of America 98 13734 13738 DOI

Dekkers JCM 2004 Commercial application of marker- and gene assisted selection in livestock: strategies and lessons. Journal of Animal Science 82 E313 E328

Donaldson L Vuocolo T Gray C Strandberg Y Reverter A McWilliam S Wang Y Byrne K Tellam R 2005 Construction and validation of a Bovine Innate Immune Microarray. BMC Genomics 6 135
DOI

Eggen A Fries R 1995 An integrated cytogenetic and meiotic map of the bovine genome. Animal Genetics 26 215 236

Everts-van der Wind A Kata SR Band MR Rebeiz M Larkin DM et al 2004 A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates. Genome Research 14 1424 1437
DOI

Everts-van der Wind A Larkin DM Green CA Elliott JS Olmstead CA Chiu R Schein JE Marra MA Womack JE Lewin HA 2005 A high-resolution whole-genome cattle–human comparative map reveals details of mammalian chromosome evolution. Proceedings of the National Academy of Sciences of the United States of America 102 18526 18531 DOI

Farh KK Grimson A Jan C Lewis BP Johnston WK Lim LP Burge CB Bartel DP 2005 The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science 310 1817 1821 DOI

Fazzari MJ Greally JM 2004 Epigenomics beyond CpG islands. Nature Reviews. Genetics 5 446 455 DOI

Flaherty L Herron B Symula D 2005 Genomics of the future: identification of quantitative trait loci in the mouse. Genome Research 15 1741 1745 DOI

Freking BA Murphy SK Wylie AA Rhodes SJ Keele JW Leymaster KA Jirtle RL Smith TPL 2002 Identification of the single base change causing the callipyge muscle hypertrophy phenotype, the only known example of polar overdominance in mammals. Genome Research 12 1496 1506 DOI

Galdzicka M Patnala S Hirshman MG Cai JF Nitowsky H Egeland JA Ginns EI 2002 A new gene, EVC2, is mutated in Ellis-van Creveld syndrome. Molecular Genetics and Metabolism 77 291 295 DOI

Georges M Nielsen D Mackinnon M Mishra A Okimoto R et al 1995 Mapping quantitative trait loci controlling milk production in dairy cattle by exploiting progeny testing. Genetics 139 907 920

Goddard ME 2003 Animal breeding in the (post-) genomic era. Animal Science (Penicuik, Scotland) 76 353 365


Grisart B Coppieters W Farnir F Karim L Ford C et al 2002 Positional candidate cloning of a QTL in dairy cattle: identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. Genome Research 12 222 231
DOI

Grisart B Farnir F Karim L Cambisano N Kim JJ et al 2004 Genetic and functional confirmation of the causality of the DGAT1 K232A quantitative trait nucleotide in affecting milk yield and composition. Proceedings of the National Academy of Sciences of the United States of America 101 2398 2403 DOI

Grobet L Martin LJ Poncelet D Pirottin D Brouwers B et al 1997 A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle. Nature Genetics 17 71 74 DOI

Hanotte O Ronin Y Agaba M Nilsson P Gelhaus A et al 2003 Mapping of quantitative trait loci controlling trypanotolerance in a cross of tolerant West African N’Dama and susceptible East African Boran cattle. Proceedings of the National Academy of Sciences of the United States of America 100 7443 7448 DOI

Hawken RJ Barris WC McWilliam SM Dalrymple BP 2004 An interactive bovine in silico SNP database (IBISS). Mammalian Genome 15 819 827 DOI

Heaton MP Harhay GP Bennett GL Stone RT Grosse WM Casas E Keele JW Smith TP Chitko-McKown CG Laegreid WW 2002 Selection and use of SNP markers for animal identification and paternity analysis in U.S. beef cattle. Mammalian Genome 13 272 281 DOI

Ihara N Takasuga A Mizoshita K Takeda H Sugimoto M et al 2004 A comprehensive genetic map of the cattle genome based on 3802 microsatellites. Genome Research 14 1987 1998 DOI

Ioannidis JP 2005 Why most published research findings are false. PLoS Medicine 2 e124 DOI

Itoh T Watanabe T Ihara N Mariani P Beattie CW Sugimoto Y Takasuga A 2005 A comprehensive radiation hybrid map of the bovine genome comprising 5593 loci. Genomics 85 413 424 DOI

Kambadur R Sharma M Smith TP Bass JJ 1997 Mutations in myostatin (GDF8) in double-muscled Belgian Blue and Piedmontese cattle. Genome Research 7 910 916

Kappes SM Keele JW Stone RT McGraw RA Sonstegard TS Smith TP Lopez-Corrales NL Beattie CW 1997 A second-generation linkage map of the bovine genome. Genome Research 7 235 249


Kapranov P Cawley SE Drenkow J Bekiranov S Strausberg RL Fodor SP Gingeras TR 2002 Large-scale transcriptional activity in chromosomes 21 and 22. Science 296 916 919
DOI

Khatkar MS Thomson PC Tammen I Raadsma HW 2004 Quantitative trait loci mapping in dairy cattle: review and meta-analysis. Genetics, Selection, Evolution. 36 163 190 DOI

Kruglyak L 1999 Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genetics 22 139 144 DOI

Kutzer T Leeb T Brenig B 2003 Current state of development of genome analysis in livestock. Current Genomics 4 487 525 DOI

Larkin DM Everts-van der Wind A Rebeiz M Schweitzer PA Bachman S et al 2003 A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Research 13 1966 1972

Lee MP 2005 Genome-wide analysis of allele-specific gene expression using oligo microarrays. Methods in Molecular Biology (Clifton, N.J.) 311 39 47


Lewis BP Burge CB Bartel DP 2005 Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120 15 20
DOI

Liu WS Mariani P Beattir CW Alexander LJ Ponce De Leon FA 2002 A radiation hybrid map of the bovine Y chromosome. Mammalian Genome 13 320 326 DOI

Lo HS Wang Z Hu Y Yang HH Gere S Buetow KH Lee MP 2003 Allelic variation in gene expression is common in the human genome. Genome Research 13 1855 1862

Marra MA Kucaba TA Dietrich NL Green ED Brownstein B Wilson RK McDonald KM Hillier LW McPherson JD Waterston RH 1997 High throughput fingerprint analysis of large-insert clones. Genome Research 7 1072 1084


Mattick JS 2003 Challenging the dogma: the hidden layer of non-protein coding RNAs in complex organisms. BioEssays 25 930 939
DOI

Miller GY Bartlett PC Lance SE Anderson J Heider LE 1993 Costs of clinical mastitis and mastitis prevention in dairy herds. Journal of the American Veterinary Medical Association 202 1230 1236

Modrek B Lee CJ 2003 Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nature Genetics 34 177 180
DOI

Morgan HD Sutherland HG Martin DI Whitelaw E 1999 Epigenetic inheritance at the agouti locus in the mouse. Nature Genetics 23 314 318 DOI

Paschal JC (2005) Marker assisted selection for genetic improvement. Available at http://agfacts.tamu.edu/D11/Extension/animal%20science/E-352Genetics.pdf [Verified 25 May 2007]

Pastinen T Sladek R Gurd S Sammak A Ge B et al 2004 A survey of genetic and epigenetic variation affecting human gene expression. Physiological Genomics 16 184 193 DOI

Pollak EJ 2005 Application and impact of new genetic technologies on beef cattle breeding: a ‘real world’ perspective. Australian Journal of Experimental Agriculture 45 739 748 DOI

Raadsma HW Tammen I 2005 Biotechnologies and their potential impact on animal breeding and production: a review. Australian Journal of Experimental Agriculture 45 1021 1032 DOI

Ravasi T Suzuki H Pang KC Katayama S Furuno M et al 2005 Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Research 16 11 19 DOI

Reik W Walter J 2001 Genomic imprinting: parental influence on the genome. Nature Reviews. Genetics 2 21 32 DOI

Riggs AD, Martienssen RA, Russo VEA (1996) Introduction. In ‘Epigenetic mechanisms of gene regulation’. (Eds VEA Russo, RA Martienssen, AD Riggs) p. 1. (Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY)

Ron M Kliger D Feldmesser E Seroussi E Ezra E Weller JI 2001 Multiple QTL analysis of bovine chromosome 6 in the Israeli Holstein population by a daughter design. Genetics 159 727 735

Ruiz-Perez VL Ide SE Strom TM Lorenz B Wilson D et al 2000 Mutations in a new gene in Ellis-van Creveld syndrome and Weyers acrodental dysostosis. Nature Genetics 24 283 286
DOI

Rupp R Boichard D 2003 Genetics of resistance to mastitis in dairy cattle. Veterinary Research 34 671 688 DOI

Schibler L Roig A Mahe MF Save JC Gautier M Taourit S Boichard D Eggen A Cribiu EP 2004 A first generation bovine BAC-based physical map. Genetics, Selection, Evolution. 36 105 122

Seegers H Fourichon C Beaudeau F 2003 Production effects related to mastitis and mastitis economics in dairy cattle herds. Veterinary Research 34 475 491
DOI

Smith SJ Cases S Jensen DR Chen HC Sande E Tow B Sanan DA Raber J Eckel RH Farese RV Jr 2000 Obesity resistance and multiple mechanisms of triglyceride synthesis in mice lacking DGAT1. Nature Genetics 25 87 90 DOI

Suchyta SP Sipkovsky S Kruska R Jeffers A McNulty A et al 2003 Development and testing of a high-density cDNA microarray resource for cattle. Physiological Genomics 15 158 164

Takeda H Takami M Oguni T Tsuji T Yoneda K et al 2002 Positional cloning of the gene LIMBIN responsible for bovine chondrodysplastic dwarfism. Proceedings of the National Academy of Sciences of the United States of America 99 10549 10554
DOI

The Human Genome Sequencing Consortium 2001 Initial sequencing and analysis of the human genome. Nature 409 860 921 DOI

The Rat Genome Sequencing Consortium 2004 Genome sequence of the brown Norway rat yields insights into mammalian evolution. Nature 428 493 521 DOI

Truswell AS 2005 The A2 milk case: a critical review. European Journal of Clinical Nutrition 59 623 631 DOI

Van Eenennam A (2005) Marker assisted selection in beef cattle. Available at http://animalscience.ucdavis.edu/animalbiotech/Outreach/Marker_Assisted_Selection_in_Beef_Cattle.pdf [Verified 25 May 2007]

Vuocolo T Cockett N Tellam RL 2005 Expression of imprinted genes surrounding the callipyge mutation in ovine skeletal muscle. Australian Journal of Experimental Agriculture 45 879 892 DOI

Wall RJ Powell AM Paape MJ Kerr DE Bannerman DD Pursel VG Wells KD Talbot N Hawk HW 2005 Genetically enhanced cows resist intramammary Staphylococcus aureus infection. Nature Biotechnology 23 445 451 DOI

Waterland RA Garza C 1999 Potential mechanisms of metabolic imprinting that lead to chronic disease. American Journal of Clinical Nutrition 69 179 197

Weaver IC Cervoni N Champagne FA D’Alessio AC Sharma S Seckl JR Dymov S Szyf M Meaney MJ 2004 Epigenetic programming by maternal behavior. Nature Neuroscience 7 847 854
DOI

Whitelaw E Martin DI 2001 Retrotransposons as epigenetic mediators of phenotypic variation in mammals. Nature Genetics 27 361 365 DOI

Williams JL Eggen A Ferretti L Farr CJ Gautier M et al 2002 A bovine whole-genome radiation hybrid panel and outline map. Mammalian Genome 13 469 474 DOI

Wilson HL Aich P Roche FM Jalal S Hodgson PD Brinkman FS Potter A Babiuk LA Griebel PJ 2005 Molecular analyses of disease pathogenesis: application of bovine microarrays. Veterinary Immunology and Immunopathology 105 277 287 DOI

Womack JE 2005 Advances in livestock genomics: opening the barn door. Genome Research 15 1699 1705 DOI



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