Capturing benefits from the bovine genome sequence

Australian Journal of Experimental Agriculture

Volumn 47, Issue 9, 2007, Pages 1039-1050

  Tellam, Ross L ^a  

^a CSIRO   (Australia)

Author keywords

Cow; Ruminant

Indexed keywords

CATTLE; DAIRY FARMING; GENOME; LIVESTOCK FARMING; PHENOTYPE; PHENOTYPIC PLASTICITY; POLYMORPHISM; REPRODUCTIVE STATUS; REPRODUCTIVE STRATEGY; RESOURCE USE; RUMINANT;

AUSTRALASIA; AUSTRALIA;

ANIMALIA; BOVIDAE; BOVINAE;

EID: 34547666522     PISSN: 08161089     EISSN: None     Source Type: Journal    
DOI: 10.1071/EA06032     Document Type: Conference Paper

References (85)

1. Anon. (2005) Australian dairy productions systems and profit. Available at http://www.dairyaustralia.com.au [Verified 25 May 2007]
2. Austin CP, Battey JF, Bradley A, Bucan M, Capecchi M, et al. (2004) The knockout mouse project. Nature Genetics 36, 921-924. doi:10.1038/ng0904-921
3. 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:10.1101/gr.145900
4. 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:10.1081/ABIO-120005779
5. Banks RG (2005) Challenges with investing in genetic improvement for the Australian extensive livestock industries. Australian Journal of Experimental Agriculture 45, 1033-1039. doi:10.1071/EA05072
6. 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:10.1071/EA05067
7. 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:10.1007/s003359900340
8. 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.
9. Carter N (2004) As normal as normal can be? Nature Genetics 36, 931-932. doi:10.1038/ng0904-931
10. 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:10.1007/BF00539005
11. 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:10.1038/86856
12. 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:10.1126/science.1108625
13. 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:10.1038/nature04244
14. 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:10.1016/j.dci.2003.10.002
15. 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]
16. 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:10.1038/ng1810
17. 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:10.1051/gse:2004032
18. 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:10.1101/gr.3806705
19. Collins FS, Green ED, Guttmacher AR, Guyer MS (2003) A vision for the future of genomics research. Nature 422, 835. doi:10.1038/ nature01626
20. Dalrymple BP (2005) Harnessing the bovine genome sequence for the Australian cattle and sheep industries. Australian Journal of Experimental Agriculture 45, 1011-1016. doi:10.1071/EA05043
21. 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:10.1073/pnas.241522698
22. Dekkers JCM (2004) Commercial application of marker- and gene assisted selection in livestock: strategies and lessons. Journal of Animal Science 82, E313-E328.
23. 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:10.1186/1471-2164-6- 135
24. Eggen A, Fries R (1995) An integrated cytogenetic and meiotic map of the bovine genome. Animal Genetics 26, 215-236.
25. 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:10.1101/gr.2554404
26. 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 highresolution 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:10.1073/pnas. 0509285102
27. 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:10.1126/science. 1121158
28. Fazzari MJ, Greally JM (2004) Epigenomics beyond CpG islands. Nature Reviews. Genetics 5, 446-455. doi:10.1038/nrg1349
29. 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:10.1101/gr.3841405
30. 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:10.1101/gr.571002
31. 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:10.1016/S1096-7192(02)00178-6
32. 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.
33. Goddard ME (2003) Animal breeding in the (post-) genomic era. Animal Science (Penicuik, Scotland) 76, 353-365.
34. 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:10.1101/gr.224202
35. 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:10.1073/pnas.0308518100
36. 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:10.1038/ng0997-71
37. 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:10.1073/pnas.1232392100
38. Hawken RJ, Barris WC, McWilliam SM, Dalrymple BP (2004) An interactive bovine in silico SNP database (IBISS). Mammalian Genome 15, 819-827. doi:10.1007/s00335-004-2382-4
39. 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:10.1007/s00335-001-2146-3
40. 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:10.1101/gr.2741704
41. Ioannidis JP (2005) Why most published research findings are false. PLoS Medicine 2, e124. doi:10.1371/journal.pmed.0020124
42. 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:10.1016/j.ygeno.2004.12.007
43. 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.
44. 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.
45. 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:10.1126/science.1068597
46. 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:10.1051/gse:2003057
47. Kruglyak L (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genetics 22, 139-144. doi:10.1038/9642
48. Kutzer T, Leeb T, Brenig B (2003) Current state of development of genome analysis in livestock. Current Genomics 4, 487-525. doi:10.2174/1389202033490286
49. 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.
50. Lee MP (2005) Genome-wide analysis of allele-specific gene expression using oligo microarrays. Methods in Molecular Biology (Clifton, N.J.) 311, 39-47.
51. 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:10.1016/j.cell.2004.12.035
52. 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:10.1007/s00335-001-2133-8
53. 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.
54. 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.
55. Mattick JS (2003) Challenging the dogma: the hidden layer of non-protein coding RNAs in complex organisms. BioEssays 25, 930-939. doi:10.1002/bies.10332
56. 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.
57. 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:10.1038/ng1159
58. Morgan HD, Sutherland HG, Martin DI, Whitelaw E (1999) Epigenetic inheritance at the agouti locus in the mouse. Nature Genetics 23, 314-318. doi:10.1038/15490
59. 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]
60. 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:10.1152/physiolgenomics. 00163.2003
61. 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:10.1071/EA05047
62. 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:10.1071/EA05073
63. 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:10.1101/gr.4200206
64. Reik W, Walter J (2001) Genomic imprinting: parental influence on the genome. Nature Reviews. Genetics 2, 21-32. doi:10.1038/35047554
65. 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)
66. 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.
67. 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:10.1038/73508
68. Rupp R, Boichard D (2003) Genetics of resistance to mastitis in dairy cattle. Veterinary Research 34, 671-688. doi:10.1051/vetres: 2003020
69. 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.
70. 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:10.1051/vetres:2003027
71. 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:10.1038/75651
72. 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.
73. 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:10.1073/pnas.152337899
74. The Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921. doi:10.1038/35057062
75. The Rat Genome Sequencing Consortium (2004) Genome sequence of the brown Norway rat yields insights into mammalian evolution. Nature 428, 493-521. doi:10.1038/nature02426
76. Truswell AS (2005) The A2 milk case: a critical review. European Journal of Clinical Nutrition 59, 623-631. doi:10.1038/sj.ejcn. 1602104
77. 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]
78. 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:10.1071/EA05049
79. 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:10.1038/nbt1078
80. Waterland RA, Garza C (1999) Potential mechanisms of metabolic imprinting that lead to chronic disease. American Journal of Clinical Nutrition 69, 179-197.
81. 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:10.1038/nn1276
82. Whitelaw E, Martin DI (2001) Retrotransposons as epigenetic mediators of phenotypic variation in mammals. Nature Genetics 27, 361-365. doi:10.1038/86850
83. 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:10.1007/s00335-002-3001-x
84. 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:10.1016/j.vetimm.2005.02.015
85. Womack JE (2005) Advances in livestock genomics: opening the barn door. Genome Research 15, 1699-1705. doi:10.1101/gr.3809105