Impact of High-Throughput Genotyping and Sequencing on the Identification of Genes and Variants Underlying Phenotypic Variation in Domestic Cattle

Bovine Genomics

Volumn , Issue , 2012, Pages 234-258

  Georges, Michel ^a  

^a UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

Causative mutations, underlying recessive defects; Empirical, biometrical selection, molecular substrate as "black box"; Genetic variation for traits, allele substitution at "polygenes"; Genetical genomics, causative genes underlying QTL; Genome wide SNP, resequencing in larger cohorts; High density SNP, GS related, causative DSV and genes; High throughput genotyping, variants in domestic cattle; Positional cloning, high cost, leading to IBD mapping; Positional cloning, in causative gene, variant detection; QTL based marker assisted selection

Indexed keywords

EID: 84886109262     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118301739.ch15     Document Type: Chapter

References (82)

1. 1000 Genomes Project Consortium (2010)Amap of human genome variation from populationscale sequencing. Nature 467: 1061-1073.
2. Austin, C.P., et al. (2004) The knockout mouse project. Nature Genetics 36: 921-924.
3. Barton, N.H. and Keightley, P.D. (2002). Understanding quantitative genetic variation. Nature Reviews Genetics 3: 11-21.
4. Blott, S., et al. (2003) Molecular dissection of a quantitative trait locus: a phenylalanine-totyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition. Genetics 163: 253-266.
5. Bostein, D., White, R.L., Skolnick, M., Davis, R.W. (1980) Constrcution of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32: 314-331.
6. Bovine Genome Sequencing and Analysis Consortium, et al. (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324: 522-528.
7. Bovine HapMap Consortium, et al. (2009) Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324: 528-552.
8. Byrne, K., Colgrave, M.L., Vuocolo, T., Pearson, R., Bidwell, C.A., Cockett, N.E., Lynn, D.J. Fleming-Waddell, J.N., Tellam, R.L. (2010) The imprinted retrotransposon-like gene PEG11 (RTL1) is expressed as a full-length protein in skeletal muscle from Callipyge sheep. PLoS One 5: e8638.
9. Charlier, C., et al. (1995) The mh gene causing double-muscling in cattle maps to bovine Chromosome 2. Mammalian Genome 6: 788-792.
10. Charlier, C., et al. (2008) Highly effective SNP-based association mapping and management of recessive defects in livestock. Nature Genetics 40: 449-454.
11. Charlier, C., et al. (2012) A deletion in the bovine FANCI gene compromises fertility by causing fetal death and brachyspina. Submitted for publication.
12. Clop, A., 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.
13. Cohen-Zinder, M., 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.
14. Davis, E., Jensen, C.H., Schroder, H.D., Farnir, F., Shay-Hadfield, T., Kliem, A., Cockett, N., Georges, M., Charlier, C. (2004) Ectopic expression of DLK1 protein in skeletal muscle of padumnal heterozygotes causes the callipyge phenotype. Current Biology 14: 1858-1862.
15. Dickson, S.P., Wang, K., Krantz, I., Hakonarson, H., Goldstein, D.B. (2010) Rare variants create synthetic genome-wide associations. PLoS Biology 8: e1000294.
16. Druet, T. and Georges, M. (2010) A hidden markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping. Genetics 184: 789-798
17. Dunner, S., Charlier, C., Farnir, F., Brouwers, B., Canon, J., Georges, M. (1997) Towards interbreed IBD fine mapping of the mh locus: double-muscling in the Asturiana de los Valles breed involves the same locus as in the Belgian Blue cattle breed. Mammalian Genome 8: 430-435.
18. Durkin, K., Coppieters, W., Drögemüller, C., Ahariz, N., Cambisano, N., Druet, T., Fasquelle, C., Haile, A., Horin, P., Huang, L., Kamatani, Y., Karim, L., Lathrop, M., Moser, S., Oldenbroek, K., Rieder, S., Sartelet, A., Sölkner, J., StÅlhammar, H., Zelenika, D., Zhang, Z., Leeb T., Georges, M., Charlier, C. (2012) Serial translocation by means of circular intermediates underlies colour sidedness in cattle. Nature 482: 81-84.
19. Farnir, F., et al. (2002) Simultaneous mining of linkage and linkage disequilibrium to fine map quantitative trait loci in outbred half-sib pedigrees: revisiting the location of a quantitative trait locus with major effect on milk production on bovine chromosome 14. Genetics 161: 275-287.
20. Fasquelle, C., et al. (2009) Balancing selection of a frame-shift mutation in the MRC2 gene accounts for the outbreak of the Crooked Tail Syndrome in Belgian Blue Cattle. PLoS Genetics 5: e1000666.
21. FitzGerald, R.J. (1997) Exploitation of casein variants. In: Milk Composition, Production and Biotechnology, edited by R.A.S. Welch, D.J.W. Burns, S.R. Davis, A.I. Popay, and C.G. Prosser, pp. 153-172. New York: CAB International.
22. Freking, B.A., Murphy, S.K., Wylie, A.A., Rhodes, S.J., Keele, J.W., Leymaster, K.A., Jirtle, R.L., Smith TP. (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.
23. Georges, M., et al. (1993a) Microsatellite mapping of a gene affecting horn development in Bos taurus. Nature Genetics 4: 206-210.
24. Georges, M., et al. (1993b) Microsatellite mapping of the gene causing weaver disease in cattle will allow the study of an associated quantitative trait locus. Proceedings of the National Academy of Sciences of the United States of America 90: 1058-1062.
25. Grisart, B., 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.
26. Grisart, B., 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.
27. Grobet, L., Poncelet, D., Royo, L.J., Brouwers, B., Pirottin, D., Michaux, C., Ménissier, F., Zanotti, M., Dunner, S., Georges, M. (1998) Molecular definition of an allelic series of mutations disrupting the myostatin function and causing double-muscling in cattle. Mammalian Genome 9: 210-213.
28. Grobet, L., et al. (1997) A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle. Nature Genetics 17: 71-74.
29. Hayes, B.J., Pryce, J., Chamberlain, A.J., Bowman, P.J., Goddard, M.E. (2010) Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits. PLoS Genetics 6: e1001139.
30. Hill, J.P., et al. (1997) In: Milk Composition, Production and Biotechnology, edited by R.A.S. Welch, D.J.W. Burns, S.R. Davis, A.I. Popay, and C.G. Prosser, pp. 173-203. New York: CAB International.
31. Hubner, N., et al. (2005) Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nature Genetics 37: 243-253.
32. Hugot, J.P., et al. (2001) Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature 411: 599-603
33. Kambadur, R., Sharma, M., Smith, T.P., Bass, J.J. (1997) Mutations in myostatin (GDF8) in double-muscled Belgian Blue and Piedmontese cattle. Genome Research 7: 910-916.
34. Karim, L., et al. (2011) Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nature Genetics 43: 405-413.
35. Kashi, Y., Hallerman, E., Soller, M. (1990) Marker-assisted selection of candidate bulls for progeny testing programs. Animal Production 51: 63-74.
36. Kerem, B., Rommens, J.M., Buchanan, J.A., Markiewicz, D., Cox, T.K., Chakravarti, A., Buchwald, M., Tsui LC. (1989) Identification of the cystic fibrosis gene: genetic analysis. Science 245: 1073-1080.
37. Kim, J.J., Farnir, F., Savell, J., Taylor, J.F. (2003) Detection of quantitative trait loci for growth and beef carcass fatness traits in a cross between Bos taurus (Angus) and Bos indicus (Brahman) cattle. Journal of Animal Science 81: 1933-1942.
38. Lander, E.S. and Kruglyal, L. (1995) Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nature Genetics 11: 241-247.
39. Lee, S.H., Wray, N.R., Goddard, M.E., Visscher, P.M. (2011) Estimating missing heritability for disease from genome-wide association studies. American Journal of Human Genetics 88: 294-305.
40. Lynch, M. and Walsh B. (1998) Genetic Analysis of Quantitatve Traits. Sunderland: Sinauer Associates.
41. Mackay, T.F. (2001) Quantitative trait loci in Drosophila. Nature Reviews Genetics 2: 11-20.
42. Mackinnon, M. and Georges, M. (1998) A bottom-up approach towards marker assisted selection. Livestock Production Science 54: 229-250.
43. Marchini, J. and Howie, B. (2010) Genotype imputation for genome-wide association studies. Nature Reviews Genetics 11: 499-511.
44. Mardis, E.R. (2008) Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics 9: 387-402.
45. Matukumalli, L.K., et al. (2009) Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4: e5350.
46. McPherron, A.C. and Lee, S.J. (1997) Double muscling in cattle due to mutations in the myostatin gene. Proceedings of the National Academy of Sciences of the United States of America 94: 12457-12461.
47. Merveille, A.C., et al. (2011) CCDC39 is required for assembly of inner dynein arms and the dynein regulatory complex and for normal ciliary motility in humans and dogs. Nature Genetics 43: 72-78.
48. Meuwissen, T.H. and Goddard, M.E. (2000) Fine mapping of quantitative trait loci using linkage disequilibria with closely linked marker loci. Genetics 155: 421-430.
49. Meuwissen, T.H. and Goddard, M.E. (2001) Prediction of identity by descent probabilities from marker-haplotypes. Genetics Selection Evolution 33: 605-634.
50. Meuwissen, T.H., Hayes, B.J., Goddard, M.E. (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.
51. Momozawa, Y., et al. (2011) Resequencing of positional candidates identifies low frequency IL23R coding variants protecting against inflammatory bowel disease. Nature Genetics 43: 43-47.
52. Neale, B.M., Rivas, M.A., Voight, B.F., Altshuler, D., Devlin, B., Orho-Melander, M., Kathiresan, S., Purcell, S.M., Roeder, K., Daly, M.J. (2011) Testing for an unusual distribution of rare variants. PLoS Genetics 7: e1001322.
53. Nezer, C., Collette, C., Moreau, L., Brouwers, B., Kim, J.J., Giuffra, E., Buys, N., Andersson, L., Georges, M. (2003) Haplotype sharing refines the location of an imprinted quantitative trait locus with major effect on muscle mass to a 250-kb chromosome segment containing the porcine IGF2 gene. Genetics 165: 277-285.
54. Orr, H.A. (2005). The genetic theory of adpatation: a brief history. Nature Reviews Genetics 6: 119-127.
55. Pirottin, D., Charlier, C., Georges, M., Takeda, H. (2011). Knocking the CLPG mutation in the mouse genome partially recapitulates the callipyge phenomenology. Submitted for publication.
56. Pirottin, D., et al. (1999) High-resolution, human-bovine comparative mapping based on a closed YAC contig spanning the bovine mh locus. Mammalian Genome 10: 289- 293.
57. Platt, A., Vilhjálmsson, B.J., Nordborg, M. (2010) Conditions under which genome-wide association studies will be positively misleading. Genetics 186: 1045-1052.
58. Riquet, J., et al. (1999) Fine-mapping of quantitative trait loci by identity by descent in outbred populations: application to milk production in dairy cattle. Proceedings of the National Academy of Sciences of the United States of America 96: 9252-9257.
59. Romeo, S., Pennacchio, L.A., Fu, Y., Boerwinkle, E., Tybjaerg-Hansen, A., Hobbs, H.H., Cohen, J.C. (2007) Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nature Genetics 39: 513-516.
60. Sartelet, A., Klingbeil, P., Fasquelle, C., Franklin, C., Géron, S., Isacke, C., Georges, M., Charlier, C. (2012a) Allelic heterogeneity of Crooked Tail Syndrome fits the balancing selection hypothesis. Animal Genetics in press.
61. Sartelet, A., Fasquelle, C., Géron, S., Michaux, C., Zhang, Z., Coppieters, W., Georges, M., Druet, T., Charlier, C. (2012b) A splice site mutation in the RNF11 gene causes a deficiency in innate immunity with proportionate dwarfism. PLOS Genetics in press.
62. Sax, K. (1923) The association of size differences with seed-coat pattern and igmentation in Phaseolus vulgaris. Genetics 8: 552-560.
63. Schwenger, B., Schöber, S., Simon, D. (1993) DUMPS cattle carry a point mutation in the uridine monophosphate synthase gene. Genomics 16: 241-244.
64. Service, P.M. (2004) How Good Are Quantitative Complementation Tests? Science of Aging Knowledge Environment 12: pe13.
65. Shuster, D.E., Kehrli M.E. Jr, Ackermann, M.R., Gilbert, R.O. (1992) Identification and prevalence of a genetic defect that causes leukocyte adhesion deficiency in Holstein cattle. Proceedings of the National Academy of Sciences of the United States of America 89: 9225- 9229.
66. Smit, M., Segers, K., Carrascosa, L.G., Shay, T., Baraldi, F., Gyapay, G., Snowder, G., Georges, M., Cockett, N., Charlier C. (2003) Mosaicism of Solid Gold supports the causality of a noncoding A-to-G transition in the determinism of the callipyge phenotype. Genetics 163: 453-456.
67. Steinmetz, L.M., Sinha, H., Richards, D.R., Spiegelman, J.I., Oefner, P.J., McCusker, J.H., Davis, R.W. (2002) Dissecting the architecture of a quantitative trait locus in yeast. Nature 416: 326-330.
68. Stern, D. (1998) A role of ultrabithorax in morphological differences between Drosophila species. Nature 396: 463-466.
69. Takeda, H., 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.
70. Thaller, G. and Hoeschele, I. (2000) Fine-mapping of quantitative trait loci in half-sib families using current recombinations. Genetical Research 76: 87-104.
71. The Huntington's Disease Collaborative Research Group (1993) A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. Cell 72: 971-983.
72. Thoday, J.M. (1961) Location of polygenes. Nature 191: 368-370.
73. Thomsen, B., Horn, P., Panitz, F., Bendixen, E., Petersen, A.H., Holm, L.E., Nielsen, V.H., Agerholm, J.S., Arnbjerg, J., Bendixen, C. (2006) A missense mutation in the bovine SLC35A3 gene, encoding a UDP-N-acetylglucosamine transporter, causes complex vertebral malformation. Genome Research 16: 97-105.
74. Van Laere, A.S., et al. (2003) A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425: 832-836.
75. VanRaden, P.M., Van Tassell, C.P., Wiggans, G.R., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Schenkel, F.S. (2009) Invited review: reliability of genomic predictions for North American Holstein Bulls. Journal of Dairy Science 92: 16-24.
76. Voz, M., Coppieters, W., Mafroid, I., Baudhuin, A., Cahrlier, C., Meyer, D., Driever, W., Martial, J., Peers, B. (2012) Effective NGS-based identification of ENU-induced mutations in zebrafish. Submitted for publication.
77. Weber, J.L. and May, P.E. (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. American Journal of Human Genetics 44: 388-396.
78. Weller, J.I., Kashi, Y., Soller, M. (1990) Power of daughter and grand-daughter desgns for dtermining linkage between marker loci and quantitatve trait loci in dairy cattle. Journal of Dairy Science 73: 2525-2537.
79. Winter, A., Krämer, W., Werner, F.A., Kollers, S., Kata, S., Durstewitz, G., Buitkamp, J., Womack, J.E., Thaller, G., Fries R. (2002) ssociation of a lysine-232/alanine polymorphism in a bovine gene encoding acyl-CoA:diacylglycerol acyltransferase (DGAT1) with variation at a quantitative trait locus for milk fat content. Proceedings of the National Academy of Sciences of the United States of America 99: 9300-9305.
80. Yalcin, B., Willis-Owen, S.A., Fullerton, J., Meesaq, A., Deacon, R.M., Rawlins, J.N., Copley, R.R., Morris, A.P., Flint, J., Mott, R. (2004) Genetic dissection of a behavioral quantitative trait locus shows that Rgs2 modulates anxiety in mice. Nature Genetics 36: 1197-1202.
81. Yang, J., et al. (2010) Common SNPs explain a large proportion of the heritability for human height. Nature Genetics 42: 565-569.
82. Zhang, Z., Sartelet, A., Charlier, C., Georges, M., Farnir, F., Druet, T. (2012) Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification. Submitted for publication.