Bayesian genome-wide association analysis of growth and yearling ultrasound measures of carcass traits in brangus heifers

Journal of Animal Science

Volumn 90, Issue 10, 2012, Pages 3398-3409

  Peters, S O ^a,b   Kizilkaya, K ^c,d   Garrick, D J ^c,e   Fernando, R L ^c   Reecy, J M ^c   Weaber, R L ^b,g   Silver, G A ^a   Thomas, M G ^a,f,h  

^a NEW MEXICO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF MISSOURI   (United States)

^c IOWA STATE UNIVERSITY   (United States)

^d ADNAN MENDERES UNIVERSITY   (Turkey)

^e MASSEY UNIVERSITY   (New Zealand)

^f Veterinary Dentistry and Oral Surgery   (United States)

^g BERRY COLLEGE   (United States)

^h KANSAS STATE UNIVERSITY   (United States)

Author keywords

Cattle; Genome; Growth; Quantitative trait loci; Single nucleotide polymorphism

Indexed keywords

BOS; BOS INDICUS; BOS TAURUS;

EID: 84882663585     PISSN: 00218812     EISSN: 15253163     Source Type: Journal    
DOI: 10.2527/jas.2011-4507     Document Type: Article

References (62)

1. Ahmed, S. F., and C. Farquharson. 2010. Review: the effect of GH and IGF1 on linear growth and skeletal development and their modu-lation by SOCS proteins. J. Endocrinol. 206:249-259.
2. Allan, M. F., R. M. Thallman, R. A. Cushman, S. E. Echternkamp, S. N. White, L. A. Kuehn, E. Casas, and T. P. L. Smith. 2007. Association of a single nucleotide polymorphism in SPP1 with growth traits and twinning in a cattle population selected for twinning rate. J. Anim. Sci. 85:341-347.
3. Arias, J. A., M. Keehan, P. Fisher, W. Coppieters, and R. Spelman. 2009. A high density linkage map of the bovine genome. BMC Genet. 10:18.
4. Balding, D. J. 2006. A tutorial on statistical methods for population association studies. Nat. Rev. Genet. 7:781-791.
5. Beauchemin, V. R., M. G. Thomas, D. E. Franke, and G. A. Silver. 2006. Evaluation of DNA polymorphisms involving growth hor-mone relative to growth and carcass characteristics in Brahman steers. Genet. Mol. Res. 5:438-447.
6. Bolormaa, S., B. J. Hayes, R. J. Hawken, Y. Zhang, A. Reverter, and M. E. Goddard. 2011b. Detection of chromosome segments of zebu and taurin origin and their effect on beef production and growth. J. Anim Sci. 89:2050-2060.
7. Bolormaa, S., B. J. Hayes, K. Savin, R. Hawken, W. Barendse, P. F. Arthur, R. M. Herd, and M. E. Goddard. 2011a. Genome-wide association studies for feedlot and growth traits in cattle. J. Anim. Sci. 89:1684-1697.
8. Bolormaa, S., L. R. Porto Neto, Y. D. Zhang, R. J. Bunch, B. E. Harrison, M. E. Goddard, and W. Barendes. 2011c. A genome wide association study of meat and carcass traits in Australian cattle. J. Anim. Sci. 89:2297-2309.
9. Brangus Herd Improvement Records. 2010. Accessed Jan. 1, 2010. http://www.int-Brangus.org.
10. Cantor, R. M., K. Lange, and J. S. Sinsheimer. 2010. Prioritizing GWAS results: A review of statistical methods and recommenda-tions for their applications. Am. J. Hum. Genet. 86:6-22.
11. Casas, E., S. D. Shackelford, J. W. Keele, M. Koohmaraie, T. P. L. Smith, and R. T. Stone. 2003. Detection of quantitative trait loci for growth and carcass composition in cattle. J. Anim. Sci. 81:2976-2983.
12. CattleQTLdb. 2011. Release 14. Accessed June 6, 2011. http://www.animalgenome.org/cgi-bin/QTLdb/BT/index.dbSNP. 2011. dbSNP build 133 for cow txid 9913. Accessed June 6, 2011. http://www.ncbi.nlm.nih.gov/projects/SNP.
13. DeAtley, K. L., G. Rincon, C. R. Farber, J. F. Medrano, P. Luna-Nevarez, R. M. Enns, D. M. VanLeeuwen, G. A. Silver, and M. G. Thomas. 2011. Genetic analyses involving microsatellite ETH10 genotypes on bovine chromosome 5 and performance trait measures in Angus and Brahman-influenced cattle. J. Anim. Sci. 89:2031-2041.
14. Dodenhoff, J., L. D. Van Vleck, S. D. Kachman, and R. M. Koch. 1998. Parameter estimates for direct, maternal and grandmaternal genetic effects for birthweight and weaning weight in Hereford cattle. J. Anim. Sci. 76:2521-2527.
15. Eberlein, A., A. Takasuga, K. Setoguchi, R. Pfuhl, K. Flisikowski, R. Fries, N. Klopp, R. Furbass, R. Weikard, and C. Kuhn. 2009. Dissection of genetic factors modulating fetal growth in cattle in-dicates a substantial role of the Non-SMC condensing I complex subunit G (NCAGP) gene. Genetics 183:951-964.
16. Fan, B., S. K. Onteru, Z.-Q. Du, D. J. Garrick, K. J. Stalder, and M. F. Rothschild. 2011. Genome-wide association study identifies loci for body composition and structural soundness traits in pigs. PLoS One 6:e14726.
17. Farber, C. R., P. M. Corva, and J. F. Medrano. 2006. Genome-wide isolation of growth and obesity QTL using mouse speed congenic strains. BMC Genomics 7:1-17.
18. Fernando, B. L., and D. J. Garrick. 2009. User manual for a portfo-lio of genomic selection related analyses. Animal Breeding and Genetics, Iowa State University, Ames. Accessed June 6, 2011. http://taurus.ansci.iastate.edu/Site/Welcome.html.
19. Fernando, R. L., D. Habier, C. Stricker, J. C. M. Deckers, and L. R. Totir. 2007. Genomic selection. Special issue: statistics in animal breeding and quantitative genetics: the next 60 years. Acta. Agric. Scand., Sect. A-Animal Science. 57:192-195.
20. Fernando, R. L., D. Nettleton, B. R. Southey, J. C. M. Deckers, M. F. Rothschild, and M. Soller. 2004. Controlling the proportion of false positives in multiple dependent tests. Genetics 166:611-619.
21. Garrett, A. J., G. Rincon, J. F. Medrano, M. A. Elzo, G. A. Silver, and M. G. Thomas. 2008. Promoter region of the bovine growth hor-mone receptor gene: single nucleotide polymorphism discovery in cattle and association with performance in Brangus bulls. J. Anim. Sci. 86:3315-3323.
22. Garrick, D. 2009. The revolution in genetic improvement. Lohmann Information 45:9-17.
23. Georges, M. 2007. Mapping, fine mapping, and molecular dissec-tion of quantitative trait loci in domestic animals. Annu. Rev. Genomics Hum. Genetic. 8:131-62.
24. Gibbs, R. A., J. F. Taylor, C. P. Van Tassell, W. Barendse, K. A. Eversol, C. A. Gill, R. D. Green, D. L. Hamernik, S. M. Kappes, S. Lien, L. K. Matukumalli, J. C. McEwan, L. V. Nazareth, R. D. Schnabel, G. M. Weinstock, D. A. Wheeler, P. Ajmone-Marsan, P. J. Boettcher, A. R. Caetano, J. F. Garcia, O. Hanotte, P. Mariani, L. C. Skow, J. L. Williams, B. Diallo, L. Hailemariam, M. L. Martinez, C. A. Morris, L. O. C. Silva, R. J. Spellman, W. Mulatu, K. Y. Zhao, C. A. Abbey, M. Agaba, F. R. Araujo, R. J. Bunch, J. Burton, C. Gorni, H. Olivier, B. E. Harrison, B. Luff, M. A. Machado, J. Mwakaya, G. Plastow, W. Sim, T. Smith, T. S. Stonstegard, M. B. Thomas, A. Valentini, P. Williams, J. Womack, J. A. Wooliams, Y. Liu, X. Qin, K. C. Worley, C. Gao, H. Y. Jiang. S. S. Moore, Y. R. Ren, X. Z. Song, C. D. Bustamante, R. D. Hernandez, D. M. Muzny, S. Patil, A. S. Lucas, Q. Fu, M. P. Kent, R. Vega, A. Matukumalli, S. McWilliam, G. Sclep, K. Bryc, J. Choi, H. Gao, J. J. Grefenstette, B. Murdoch, A. Stella, R. Villa-Angulo, M. Wright, J. Aerts, O. Jann, R. Negrini, M. E. Goddard, B. J. Hayes, D. G. Bradley, M. B. da Silva, L. P. L. Lau, G. E. Liu, D. J. Lynn, F. Panzitta, and K. G. Dodds. 2009. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324:528-532.
25. Goddard, M. E., and B. J. Hayes. 2009. Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat. Rev. Genet. 10:381-391.
26. Habier, D., R. L. Fernando, K. Kizilkaya, and D. J. Garrick. 2011. Extension of the Bayesian alphabet for genomic selection. BMC Bioinformatics 12:186.
27. Hawken, R. J., Y. D. Zhang, M. R. S. Fortes, E. Collis, W. C. Barris, N. J. Corbet, P. J. Williams, G. Fordyce, R. G. Holroyd, J. R. W. Walkey, W. Barendse, D. J. Johnston, K. C. Prayaga, B. Tier, A. Reverter, and S. A. Lehnert. 2012. Genome-wide association studies of female reproduction in tropically adapted beef cattle. J. Anim. Sci. 90:1398-1410.
28. Hayes, B. J., P. J. Bowman, A. J. Chamberlain, and M. E. Goddard. 2009. Invited review: genomic selection in dairy cattle: progress and challenges. J. Dairy Sci. 92:433-443.
29. Hayes, B., and M. Goddard. 2010. Genome-wide association and ge-nomic selection in animal breeding. Genome 53:876-883.
30. He, W., R. L. Fernando, J. C. M. Deckers, and H. Gilbert. 2010. A gene frequency model for QTL mapping using Bayesian infer-ence. Genet. Sel. Evol. 42:21.
31. Hu, Z. L., E.R. Fritz, and J. M. Reecy. 2007. AnimalQTLdb: A live-stock QTL database tool set for positional QTL information min-ing and beyond. Nucleic Acid Res. 35:D604-D609.
32. Imumorin, I. G., E.-H. Kim, Y.-M. Lee, D.-J. De Konig, J. A. van Arendonk, M. De Donato, J. F. Taylor, and J.-J. Kim. 2011. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits. Front. Genet. 2:44.
33. Karim, L., H. Takeda, L. Lin, T. Druet, J. A. C. Arias, D. Burain, N. Cambisano, S. R. Davis, F. Farnir, B. Grisart, B. L. Harris, M. D. Keehan, M. D. Littlejohn, R. J. Spelman, and M. Georges, and W. Coppieters. 2011. Variants modulating the expression of a chro-mosome domain encompassing PLAG1 influence bovine stature. Nat. Genet. 43:405-413.
34. Kim, J. J., F. Farner, J. Savell, and J. F. Taylor. 2003. Detection of quantitative trait loci for growth and beef fatness traits in a cross between Bos taurus (Angus) and Bos indicus (Brahman) Cattle. J. Anim. Sci. 81:1933-1942.
35. Kizilkaya, K., R. L. Fernando, and D. J. Garrick. 2010. Genomic pre-diction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism geno-types. J. Anim. Sci. 88:544-551.
36. Kuhn, C., J. Bennewitz, N. Reinsch, N. Xu, H. Thomsen, C. Looft, G. A. Brockmann, M. Schwerin, C. Weimann, S. Hiendleder, G. Erhardt, I. Medjugorac, M. Forster, B. Brenig, F. Reinhardt, R. Reents, I. Russ, G. Averdunk, J. Blumel, and E. Kalm. 2003. Quantitative trait loci mapping of functional traits in the German Holstein cattle population. J. Dairy Sci. 86:360-368.
37. Lancaster, P. A., G. E. Carstens, D. H. Crews, T. H. Welsh, T. D. A. Forbes, D. W. Forrest, L. O. Tedeschi, R. D. Randel, and F. M. Rouquette. 2009. Phenotypic and genetic relationships of resid-ual feed intake with performance and ultrasound carcass traits in Brangus heifers. J. Anim. Sci. 87:3887-3896.
38. Luna-Nevarez, P., D. W. Bailey, C. C. Bailey, D. M. VanLeeuwen, R. M. Enns, G. A. Silver, K. L. DeAtley, and M. G. Thomas. 2010. Growth characteristics, reproductive performance, and evalu-ation of their associative relationships in Brangus cattle man-aged in a Chihuahuan Desert production system. J. Anim. Sci. 88:1891-1904.
39. Luna-Nevarez, P., G. Rincon, J. F. Medrano, D. G. Riley, C. C. Chase, S. W. Coleman, D. M. VanLeeuwen, K. L. DeAtley, A. Ilsa-Trejo, G. A. Silver, and M. G. Thomas. 2011. Single nucleotide polymor-phisms in the growth hormone-insulin-like growth factor axis in straightbred and crossbred Angus, Brahman, and Romosinuano heifers: population genetic analyses and association of genotypes with reproductive phenotypes. J. Anim. Sci. 89:926-934.
40. Mai, M. D., G. Sahana, F. B. Christiansen, and B. Guldbrandtsen. 2010. A genome-wide association study for milk production traits in Danish Jersey cattle using a 50K single nucleotide polymorphism chip. J. Anim. Sci. 88:3522-3528.
41. Marques, E., J. D. Nkrumah, E. L. Sherman, and S. S. Moore. 2009. Polymorphism in positional candidate genes on BTA 14 and 26 affect carcass quality in beef cattle. J. Anim. Sci. 87:2475-2484.
42. Matukumalli, L. K., C. T. Lawley, R. D. Schnabel, J. F. Taylor, M. F. Allan, M. P. Heaton, J. O'Connell, S. S. Moore, T. P. L. Smith, T. S. Sonstegard, and C. P. Van Tassell. 2009. Development and characterization of high density SNP genotyping assay for cattle. PLoS One 4:e5350.
43. McClure, M. C., N. S. Morsci, R. D. Schnabel, J. W. Kim, P. Yao, M. M. Rolf, S. D. McKay, S. J. Gregg, R. H. Chapple, S. L. Northcutt, and J. F. Taylor. 2010. A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle. Anim. Genet. 41:597-607.
44. Moser, D. W., J. K. Bertrand, I. Misztal, L. A. Kriese, and L. L. Benyshek. 1998. Genetic parameter estimates for carcass and yearling ultrasound measurements in Brangus cattle. J. Anim. Sci. 76:2542-2548.
45. Ogorevc, J., T. Kunej, A. Razpet, and P. Dovc. 2009. Database of cat-tle candidate genes and genetic markers for milk production and mastitis. Anim. Genet. 40:832-851.
46. Olsen, H. G., B. J. Hayes, M. P. Kent, T. Nome, M. Svendsen, and S. Lien. 2010. A genome wide association study for QTL affect-ing direct and maternal effects of stillbirth and dystocia in cattle. Anim. Genet. 41:273-280.
47. Onteru, S. K., B. Fan, M. T. Nikkila, D. J. Garrick, K. J. Stalder and M. F. Rothschild. 2011. Whole-genome association analyses for lifetime reproductive traits in pig. J. Anim. Sci. 89:988-995.
48. Pannier, L., A. M. Mullen, R. M. Hamill, P. C. Stapleton, and T. Sweeney. 2010. Association analysis of single nucleotide poly-morphisms in DGAT1, TG, and FABP4 genes and intramuscular fat in crossbred Bos taurus cattle. Meat Sci. 85:515-518.
49. Rawlings, J. S., K. M. Rosler, and D. A. Harrison. 2004. The JAK/STAT signaling pathway. J. Cell Sci. 117:1281-1283.
50. Rincon, G., E. A. Farber, C. R. Farber, J. D. Nkrumah, and J. F. Medrano. 2009. Polymorphisms in the STAT6 gene and their association with carcass traits in feedlot cattle. Anim. Genet. 40:878-882.
51. Rosenberg, N. A., L. Huang, E. M. Jewett, Z. A. Szpiech, I. Jankovic, and M. Boehnke. 2011. Genome-wide association studies in di-verse populations. Nat. Rev. Genet. 11:356-366.
52. Schindler, C., and C. Plumlee. 2008. Interferons pen the JAK-STAT pathway. Semin. Cell Dev. Biol. 19:311-318.
53. Setoguchi, K., M. Furuta, T. Hirano, T. Nagao, T. Watanabe, Y. Sugimoto, and A. Takasuga. 2009. Cross-breed comparison identified a critical 591-kb region for bovine carcass weight QTL (CW-2) on chromosome 6 and Ile-442 substitution in NCAPG as a positional candidate. BMC Genet. 10:43.
54. Shirley, K. L., M. G. Thomas, D. H. Keisler, D. M. Hallford, D. M. Montrose, G. A. Silver, and M. D. Garcia. 2006. Case study: A Chihuahuan desert Brangus breeding program: Feed efficiency, metabolic hormones, and puberty in heifers sired by bulls with differing expected progeny differences for growth and scrotal cir-cumference. Prof. Anim. Sci. 22:48-58.
55. Snelling, W. M., M. F. Allan, J. W. Keele, L. A. Kuehn, T. McDaneld, T. P. L. Smith, T. S. Sonstegard, R. M. Thallman, and G. L. Bennett. 2010. Genome-wide association study of growth in crossbred beef cattle. J. Anim. Sci. 88:837-848.
56. Stelzleni, A. M., T. L. Perkins, A. H. Brown, F. W. Pohlman, Z. B. Johnson, and B. A. Sandelin. 2002. Genetic parameter estimates of yearling live animal ultrasonic measurements in Brangus cat-tle. J. Anim. Sci. 80:3150-3153.
57. Stromberg, U. L. F. 2009. Emperical Bayes and semi-Bayes ad-justments for a vast number of estimations. Eur. J. Epidemol. 24:737-741.
58. Thomas, M. G., R. M. Enns, K. L. Shirley, M. D. Garcia, A. J. Garrett, and G. A. Silver. 2007. Association of DNA polymorphisms in growth hormone and its transcriptional regulators with growth and carcass traits in two populations of Brangus bulls. Genet. Mol. Res. 6:222-237.
59. Toosi, A., R. L. Fernando, and J. C. M. Deckers. 2010. Genomic selec-tion in admixed and crossbred populations. J. Anim. Sci. 88:32-46.
60. Van Eenennaam, A. L., J. Li, R. M. Thallman, R. L. Quaas, M. E. Dikeman, C. A. Gill, D. E. Franke, and M. G. Thomas. 2007. Validation of commercial DNA tests for quantitative beef traits. J. Anim. Sci. 85:891-900.
61. Wakefield, J. 2008. Bayes factors for genome-wide association studies: comparison with P-values. Genet. Epidemol. 33:79-86.
62. White, S. N., E. Casas, M. F. Allan, J. W. Keele, W. M. Snelling, T. L. Wheeler, S. D. Shackelford, M. Koohmaraie, and T. P. L. Smith. 2007. Evaluation in beef cattle of six deoxyribonucleic acid mark-ers developed for dairy traits reveals an osteopontin polymorphism associated with postweaning growth. J. Anim. Sci. 85:1-10.