Identification of genetic markers for fat deposition and meat tenderness on bovine chromosome 5: Development of a low-density single nucleotide polymorphism map

Journal of Animal Science

Volumn 83, Issue 10, 2005, Pages 2280-2288

  Stone, R T ^a   Casas, E ^a,b   Smith, T P L ^a   Keele, J W ^a   Harhay, G ^a   Bennett, G L ^a   Koohmaraie, M ^a   Wheeler, T L ^a   Shackelford, S D ^a   Snelling, W M ^a  

^a U S MEAT ANIMAL RESEARCH CENTER   (United States)

^b NONE   (United States)

Author keywords

Bovine; Carcass Traits; Haplotype; Single Nucleotide Polymorphism

Indexed keywords

ANIMALIA; BACTERIA (MICROORGANISMS); BOS TAURUS; BOVINAE;

EID: 25444486610     PISSN: 00218812     EISSN: None     Source Type: Journal    
DOI: 10.2527/2005.83102280x     Document Type: Article

References (24)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215(3):403-410.
2. Barendse, W., R. Bunch, M. Thomas, S. Armitage, S. Baud, and N. Donaldson. 2004. The TG5 thyroglobulin gene test for a marbling quantitative trait loci evaluated in feedlot cattle. Aust. J. Exp. Agric. 44:669-674.
3. Buchanan, F. C., C. J. Fitzsimmons, A. G. Van Kessel, T. D. Thue, and S. M. Schmutz. 2002. A missense mutation in the bovine leptin gene affects carcass fat content and mRNA levels. Genet. Sel. Evol. 34:105-106.
4. Casas, E., S. D. Shackelford, J. W. Keele, R. T. Stone, S. M. Kappes, and M. Koohmaraie. 2000. Quantitative trait loci affecting growth and carcass composition of cattle segregating alternate forms of myostatin. J. Anim. Sci. 78:560-569.
5. Cundiff, L. V., T. L. Wheeler, K. E. Gregory, S. D. Shackelford, M. Koohmaraie, R. M. Thallman, G. D. Snowder, and L. D. Van Vleck. 2004. Preliminary results form Cycle VII of the cattle germplasm evaluation program at the Roman L. Hruska U. S. Meat Animal Research Center. Germplasm Evaluation Program Progress Report No. 22. USDA-ARS, Clay Center, NE.
6. Gordon, D., C. Abajian, and P. Green. 1998. Consed: A graphical tool for sequence finishing. Genome Res. 8:195-202.
7. Heaton, M. P., C. G. Chitko-McKown, W. M. Grosse, J. W. Keele, J. E. Keen and W. W. Laegreid. 2001. Interleukin-8 haplotype structure from nucleotide sequence variation in commercial populations of U.S. beef cattle. Mamm. Genome 12:219-226.
8. Kappes, S. M., J. W. Keele, R. T. Stone, R. A. McGraw, T. S. Sonstegard, T. P. L. Smith, N. L. Lopez-Corrales, and C. W. Beattie. 1997. A second-generation linkage map of the bovine genome. Genome Res. 7:235-249.
9. Larkin, D. M., A. Everts-van der Wind, M. Rebeiz, P. A. Schweitzer, S. Bachman, C. Green, C. L. Weight, E. J. Campos, L. D. Benson, J. Edwards, L. Liu, K. Osoegawa, J. E. Womack, P. J. de Jong, and H. A. Lewin. 2003. A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Res. 13:1966-1972.
10. Li, C., J. Basarab, W. M. Snelling, B. Benkel, J. Kneeland, B. Murdoch, C. Hansen, and S. S. Moore. 2004. Identification and fine mapping of quantitative trait loci for backfat on bovine chromosomes 2, 5, 6, 19, 21, and 23 in a commercial line of Bos taurus, J. Anim. Sci. 82:967-972.
11. Page, B. T., E. Casas, M. P. Heaton, M. G. Cullen, D. L. Hyndman, C. A. Morris, A. M. Crawford, T. L. Wheeler, M. Koohmaraie, J. W. Keele, and T. P. L. Smith. 2002. Evaluation of single-nucleotide polymorphisms in CAPN1 for association with meat tenderness in cattle. J. Anim. Sci. 80:3077-3085.
12. Page, B. T., E. Casas, R. L. Quaas, R. M. Thallman, T. L. Wheeler, S. D. Shackelford, M. Koohmaraie, S. N. White, G. L. Bennett, J. W. Keele, M. E. Dikeman, and T. P. L. Smith. 2004. Association of markers in the bovine CAPN1 gene with meat tenderness in large crossbred populations that sample influential industry sires. J. Anim. Sci. 82:3474-3481.
13. Reich, D. E., M. Cargill, S. Bolk, J. Ireland, P. C. Sabeti, D. J. Richter, T. Lavery, R. Kouyoumjian, S. F. Farhadian, R. Ward, and E. S. Lander. 2001. Linkage disequilibrium in the human genome. Nature 411:199-204.
14. Seltman, H., K. Roeder, and B. Devlin. 2003. Evolutionary-based association analysis using haplotype data. Genet. Epidemiol. 25:48-58.
15. Shackelford, S. D., L. V. Cundiff, K. E. Gregory, and M. Koohmaraie. 1995. Predicting beef carcass cutability. J. Anim. Sci. 73:406-413.
16. Siefert, W., P. Forster, K. H. Jockel, D. A. Mvere, B. Brinkmann, C. Naber, R. Crookes, A. Du, P. Heyns, J. T. Epplen, J. Fridey, B. I. Freedman, N. Mueller, D. Stolks, A. M. Sharma, K. Al Moutaery, H. Grosse-Wilde, B. Buerbaum, T. Ehrlich, H. R. Ahmad, B. Horsthemke, E. D. Du Toit, A. Tiilikainen, J. Ge, Y. Wang, and D. Rosskopft. 1999. Worldwide ethnic distribution of the G protein beta3 subunit 825T allele and its association with obesity in Caucasian, Chinese, and Black African individuals. J. Am. Soc. Nephrol. 10(9):1921-1930.
17. Smith, T. P. L., W. M. Grosse, B. A. Freking, A. J. Roberts, R. T. Stone, E. Casas, J. E. Wray, J. White, J. Cho, S. C. Fahrenkrug, G. L. Bennett, M. P. Heaton, W. W. Laegreid, G. A. Rohrer, C. G. Chitko-McKown, G. Pertea, I. Holt, S. Karamycheva, F. Liang, J. Quackenbush, and J. W. Keele. 2001. Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle. Genome Res. 11:626-630.
18. Snelling, W. M., E. Casas, R. T. Stone, T. P. L. Smith, J. W. Keele, G. P. Harhay, and G. L. Bennett. 2005. Linkage mapping bovine EST-based SNP. BMC Genom. 6:74. Online. Available: http://www.biomedcentral.com/content/pdf/1471- 2164-6-74.pdf. Accessed May 17, 2005.
19. Stephens, M., and P. Donnelly. 2003. A comparison of Bayesian methods for haplotype reconstruction. Am. J. Hum. Genet. 73:1162-1169.
20. Stephens, M., N. J. Smith, and P. Donnelly. 2001. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68:978-989.
21. Stone, R. T., J. W. Keele, S. D. Shackelford, S. M. Kappes, and M. Koohmaraie. 1999. A primary screen of the bovine genome for quantitative trait loci affecting carcass and growth traits. J. Anim. Sci. 77:1379-1384.
22. Wheeler, T. L., L. V. Cundiff, S. D. Shackelford, and M. Koohmaraie. 2005. Characterization of biological types of cattle (Cycle VII): Carcass, yield, and longissimus palatability traits. J. Anim. Sci. 83:196-207.
23. Wheeler, T. L., S. D. Shackelford, and M. Koohmaraie. 1998. Cooking and palatability traits of beef longissimus steaks cooked with a belt grill or an open hearth electric broiler. J. Anim. Sci. 76:2805-2810.
24. Wiltshire, T., M. T. Pletcher, S. Batalov, S. Whitney Barnes, L. M. Tarantino, M. P. Cooke, H. Wu, K. Smylie, A. Santrosyan, N. G. Copeland, N. A. Jenkins, F. Kalush, R. J. Mural, R. J. Glynne, S. A. Kay, M. D. Adams, and C. F. Fletcher. 2003. Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse. Proc. Natl. Acad. Sci. USA 100:3380-3385.