Candidate genes and single nucleotide polymorphisms associated with variation in residual feed intake in beef cattle

Journal of Animal Science

Volumn 91, Issue 8, 2013, Pages 3502-3513

  Karisa, B K ^a   Thomson, J ^a,b   Wang, Z ^a   Stothard, P ^a   Moore, S S ^a,c   Plastow, G S ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

^b MONTANA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Beef cattle; Candidate genes; Gene networks; Residual feed intake

Indexed keywords

EID: 84882613303     PISSN: 00218812     EISSN: 15253163     Source Type: Journal    
DOI: 10.2527/jas.2012-6170     Document Type: Article

References (55)

1. Aaronson, D. S., and C. M. Horvath. 2002. A road map for those who don't know JAK-STAT. Science 296:1653-1655.
2. Ahola, J. K., L. T. Campbell, J. I. Szasz, T. A. Skow, C. W. Hunt, J. B. Glaze Jr., and R. A. Hill. 2007. Relationship between residual feed intake and meat quality in steer progeny of divergent intramuscular fat EPD Angus bulls. Proc., Annu. Meet.-Am. Soc. Anim. Sci., West. Sect. 58:193-199.
3. Allais, S., H. Levéziel, N. Payet-Duprat, J. F. Hocquette, J. Lepetit, S. Rousset, C. Denoyelle, C. Bernard-Capel, L. Journaux, A. Bonnot, and G. Renand. 2010. The two mutations, Q204X and nt821, of the myostatin gene affect carcass and meat quality in young heterozygous bulls of French beef breeds. J. Anim. Sci. 88:446-454.
4. Arnold, K., B. Lorenza, K. Jürgen, and S. Torsten. 2006. The SWISSMODEL workspace: A web-based environment for protein structure homology modeling. Bioinformatics 22:195-201.
5. Ashburner, M., C. A. Ball, J. A. Blake, D. Botstein, H. Butler, M. J. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G. M. Rubin, and G. Sherlock. 2000. Gene ontology: Tool for the unification of biology. Nat. Genet. 25:25-29.
6. Barendse, W. 2002. DNA markers for meat tenderness. Patent application WO02064820.
7. Barendse, W., A. Reverter, R. J. Bunch, B. E. Harrison, W. Barris, and M. B. Thomas. 2007. A validated whole-genome association study of efficient food utilization in cattle. J. Anim. Sci. 176:1893-1905.
8. Basarab, J. A., M. A. Price, J. L. Aalhus, E. K. Okine, W. M. Snelling, and K. L. Lyle. 2003. Residual feed intake and body composition in young growing cattle. Can. J. Anim. Sci. 83:189-204.
9. Bishop, M. D., R. C. M. Simmen, F. A. Simmen, and M. E. Davis. 1989. The relationship of insulin-like growth factor-I with post-weaning performance in Angus beef cattle. J. Anim. Sci. 67:2872-2880.
10. Bolormaa, S., B. J. Hayes, K. Savin, R. Hawken, W. Barendse, P. F. Arthur, R. M. Herd, and M. E. Goodard. 2011. Genome-wide association studies for feedlot and growth traits in cattle. J. Anim. Sci. 89:1684-1697.
11. Calvano, S. E., W. Xiao, D. R. Richards, R. M. Felciano, H. V. Baker, R. J. Cho, R. O. Chen, B. H. Brownstein, J. P. Cobb, S. K. Tschoeke, C. Miller-Graziano, L. L. Moldawer, M. N. Mindrinos, R. W. Davis, R. G. Tompkins, and S. F. Lowry. 2005. A network-based analysis of systemic inflammation in humans. Nature 437:1032-1037.
12. Casas, E., S. N. White, T. L. Wheeler, S. D. Shackelford, M. Koohmaraie, D. G. Riley, C. C. Chase Jr., D. D. Johnson, and T. P. L. Smith. 2006. Effects of calpastatin and μ-calpain markers in beef cattle on tenderness traits. J. Anim. Sci. 84:520-525.
13. Chen, Y., P. F. Arthur, I. M. Barchia, K. Quinn, P. F. Parnell, and R. M. Herd. 2012. Using gene expression information obtained by quantitative real-time PCR to evaluate Angus bulls divergently selected for feed efficiency. Anim. Prod. Sci. 52:1058-1067.
14. Crews, D. H., Jr. 2006. The genetics of feed efficiency in beef cattle. In: Proc. BIF 38th Annu. Res. Symp. Annu. Meet., Choctaw, MS. p. 22-31.
15. Curi, R. A., D. A. Palmieri, L. Suguisawa, A. L. J. Ferraz, H. N. de Oliveira, L. R. Furlan, A. C. Silveira, and C. R. Lopes. 2006. Effects of GHR gene polymorphisms on growth and carcass traits in Zebu and crossbred beef cattle. Livest. Sci. 101:94-100.
16. Elzo, M. A., G. C. Lamb, D. D. Johnson, M. G. Thomas, I. Misztal, D. O. Rae, C. A. Martinez, J. G. Wasdin, and J. D. Driver. 2012. Genomic-polygenic evaluation of Angus-Brahman multibreed cattle for feed efficiency and postweaning growth using the Illumina 3K chip. J. Anim. Sci. 90:2488-2497.
17. Fujino, T., H. Asaba, M. J. Kang, Y. Ikeda, H. Sone, S. Takada, D. H. Kim, R. X. Ioka, M. Ono, H. Tomoyori, M. Okubo, T. Murase, A. Kamataki, J. Yamamoto, K. Magoori, S. Takahashi, Y. Miyamoto, H. Oishi, M. Nose, M. Okazaki, S. Usui, K. Imaizumi, M. Yanagisawa, J. Sakai, and T. T. Yamamoto. 2003. Low-density lipoprotein receptor-related protein 5 (LRP5) is essential for normal cholesterol metabolism and glucose-induced insulin secretion. Proc. Natl. Acad. Sci. USA 100:229-234.
18. Gallagher, S. R., and P. R. Desjardins. 2007. Quantitation of DNA and RNA with absorption and fluorescence spectroscopy. Curr. Protoc. Hum. Genet. Appendix 3.
19. Gandolfi, G., L. Pomponio, P. Ertbjerg, A. H. Karlsson, L. N. Costa, R. Lametsch, V. Russo, and R. Davoli. 2011. Investigation on CAST, CAPN1 and CAPN3 porcine gene polymorphisms and expression in relation to post-mortem calpain activity in muscle and meat quality. Meat Sci. 88:694-700.
20. Gilmour, A. R., B. J. Gogel, B. R. Cullis, and R. Thompson. 2009. ASReml user guide release 3.0. VSN International Ltd., Hemel Hempstead, UK.
21. Goonewardene, L. A., Z. Wang, M. A. Price, R. C Yang, R. T. Berg, and M. Makarechian. 2003. The effect of udder type and calving assistance on weaning traits of beef and dairy × beef calves. Livest. Prod. Sci.; 81:47-56.
22. Grant, J. R., A. S. Arantes, L. Xiaoping, and P. Stothard. 2011. Indepth annotation of SNPs arising from resequencing projects using NGS-SNP. Bioinformatics 27:2300-2301.
23. Herd, R. M., and P. F. Arthur. 2009. Physiological basis for residual feed intake. J. Anim. Sci. 87(Suppl. 14):E64-E71.
24. Holm, L., and J. Park. 2000. DaliLite workbench for protein structure comparison. Bioinformatics 16:566-567.
25. Hoque, M. A., K. Katoh, and K. Suzuki. 2009. Genetic associations of residual feed intake with serum insulin-like growth factor-I and leptin concentrations, meat quality, and carcass cross sectional fat area ratios in Duroc pigs. J. Anim. Sci. 87:3069-3075.
26. Hu, Z., C. A. Park, E. R. Fritz, and J. M. Reecy. 2010. QTLdb: A comprehensive database tool building bridges between genotypes and phenotypes. 9th World Congress on Genetics Applied to Livestock Production. Leipzig, Germany.
27. Hubbard, T. J. P., B. L. Aken, S. Ayling, B. Ballester, K. Beal, E. Bragin, S. Brent, Y. Chen, P. Clapham, L. Clarke, G. Coates, S. Fairley, S. Fitzgerald, J. Fernandez-Banet, L. Gordon, S. Gräf, S. Haider, M. Hammond, R. Holland, K. Howe, A. Jenkinson, N. Johnson, A. Kähäri, D. Keefe, S. Keenan, R. Kinsella, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, K. Megy, P. Meidl, B. Overduin, A. Parker, B. Pritchard, D. Rios, M. Schuster, G. Slater, D. Smedley, W. Spooner, G. Spudich, S. Trevanion, A. Vilella, J. Vogel, S. White, S. Wilder, A. Zadissa, E. Birney, F. Cunningham, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, J. Herrero, A. Kasprzyk, G. Proctor, J. Smith, S. Searle and P. Flicek. 2009. Ensembl 2009 Nucleic Acids Research. 37 Database issue: D690-D697.
28. Kelly, A. K., M. McGee, D. H. Crews Jr., A. G. Fahey, A. R. Wylie, and D. A. Kenny. 2009. Effect of divergence in residual feed intake on feeding behavior, blood metabolic variables, and body composition traits in growing beef heifers. J. Anim. Sci. 88:109-123.
29. Kneeland, J., C. Li, J. Basarab, W. M. Snelling, B. Benkel, B. Murdoch, C. Hansen, and S. S. Moore. 2004. Identification and fine mapping of quantitative trait loci for growth traits on bovine chromosomes 2, 6, 14, 19, 21, and 23 within one commercial line of Bos taurus. J. Anim. Sci. 82:3405-3414.
30. Koch, R. M., L. A. Swiger, D. Chambers, and K. E. Gregory. 1963. Efficiency of feed use in beef cattle. J. Anim. Sci. 22:486-494.
31. Komatsu, M., T. Itoh, Y. Fujimori, M. Satoh, Y. Miyazaki, H. Takahashi, K. Shimizu, A. E. Malau-Aduli, and M. Morita. 2011. Genetic association between GHSR1a 5′UTR-microsatellite and nt-7(C > A) loci and growth and carcass traits in Japanese Black cattle. Anim. Sci. J. 82:396-405.
32. Lancet, D., M. Safran, T. Olender, I. Dalah, T. Iny-Stein, A. Inger, A. Harel, and G. Stelzer. 2008. GeneCards tools for combinatorial annotation and dissemination of human genome information. GIACS Conference on Data in Complex Systems, Palermo. Italy.
33. Li, H., J. Ruan, and R. Durbin. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18:1851-1858.
34. Liu, Y., L. Zan, S. Zhao, Y. Xin, L. Li, W. Cui, Z. Tang, and K. Li. 2010. Molecular characterization, polymorphism of bovine ZBTB38 gene and association with body measurement traits in native Chinese cattle breeds. Mol. Biol. Rep. 37:4041-4049.
35. Lü, A., X. Hu, H. Chen, Y. Dong, and Y. Pang. 2011. Single nucleotide polymorphisms of the prolactin receptor (PRLR) gene and its association with growth traits in Chinese cattle. Mol. Biol. Rep. 38:261-266.
36. Maj, A., J. Oprzadek, A. Oprzadek, E. Dymnicki, and L. Zwierzchowski. 2004. Polymorphism in the 5′-noncoding region of the bovine growth hormone receptor gene and its association with meat production traits in cattle. Anim. Res. 53:503-514.
37. Martinez, A., N. Aldai, R. Celaya, and K. Osoro. 2010. Effect of breed body size and the muscular hypertrophy gene in the production and carcass traits of concentrate-finished yearling bulls. J. Anim. Sci. 88:1229-1239.
38. 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.
39. McDonagh, M. D. 1998. Calpain activity affects muscle protein turnover and meat tenderisation. PhD thesis, The University of New England, Armidale, Australia.
40. McDonagh, M. D., R. M. Herd, E. C. Richardson, V. H. Oddy, J. A. Archer, and P. F. Arthur. 2001. Meat quality and the calpain system of feedlot steers following a single generation of divergent selection for residual feed intake. Aust. J. Exp. Agric. 41:1013-1021.
41. Moore, S. S., F. D. Mujibi, and E. L. Sherman. 2009. Molecular basis for residual feed intake in beef cattle. J. Anim. Sci. 87:E41-E47.
42. Morgan, J. B., T. L. Wheeler, M. Koohmaraie, J. W. Savell, and J. D. Crouse. 1993. Meat tenderness and the calpain proteolytic system in longissimus muscle of young bulls and steers. J. Anim. Sci. 71:1471-1476.
43. Mujibi, F. D. N., J. D. Nkrumah, O. N. Durunna, J. R. Grant, J. Mah, Z. Wang, J. Basarab, G. Plastow, D. H. Crews Jr., and S. S. Moore. 2011. Associations of marker panel scores with feed intake and efficiency traits in beef cattle using pre-selected single nucleotide polymorphisms. J. Anim. Sci. 89:3362-3371.
44. Naik, M. 2008. Identification and characterization of genetic markers and metabolic pathways controlling net feed efficiency in beef cattle. PhD thesis, University of Adelaide University, Australia.
45. Ng, P. C., and S. Henikoff. 2003. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 31:3812-3814.
46. Nkrumah, J. D., J. A. Basarab, M. A. Price, E. K. Okine, A. Ammoura, S. Guercio, C. Hansen, C. Li, B. Benkel, B. Murdoch, and S. S. Moore. 2004. Different measures of energetic efficiency and their phenotypic relationships with growth, feed intake, and ultrasound and carcass merit in hybrid cattle. J. Anim. Sci. 82:2451-2459.
47. Olfert, E. D., B. M. Cross, and A. A McWilliams, editors. 1993. Guide to the care and use of experimental animals. Vol. 1. 2nd ed. Canadian Council on Animal Care, Ottawa, ON.
48. Richardson, E. C., and R. M. Herd. 2004. Biological basis for variation in residual feed intake in beef cattle. 2. Synthesis of results following divergent selection. Aust. J. Exp. Agric. 44:431-440.
49. Rolf, M. M., J. F. Taylor, R. D. Schnabel, S. D. Mckay, M. C. Mc-Clure, S. L. Northcutt, M. S. Kerley, and R. L. Weaber. 2012. Genome-wide association analysis for feed efficiency in Angus cattle. Anim. Genet. 43:367-374.
50. Sherman, E. L., J. D. Nkrumah, C. Li, R. Bartusiak, B. Murdoch, and S. S. Moore. 2009. Fine mapping quantitative trait loci for feed intake and feed efficiency in beef cattle. J. Anim. Sci. 87:37-45.
51. Sherman, E. L., J. D. Nkrumah, B. M. Murdoch, and S. S. Moore. 2008. Identification of polymorphisms influencing feed intake and efficiency in beef cattle. Anim. Genet. 39:225-231.
52. Sherry, S. T., M. H. Ward, M. Kholodov, J. Baker, L. Phan, E. M. Smigielski, and K. Sirotkin. 2001. dbSNP: The NCBI database of genetic variation. Nucleic Acids Res. 29:308-311.
53. Snelling, W. M., M. F. Allan, J. W. Keele, L. A. Kuehn, R. M. Thallman, G. L. Bennett, C. L. Ferrell, T. G. Jenkins, H. C. Freetly, M. K. Nielsen, and K. M. Rolfe. 2011. Partial-genome evaluation of postweaning feed intake and efficiency of crossbred beef cattle. J. Anim. Sci. 89:1731-1741.
54. Stick, D. A., M. E. Davis, S. C. Loerch, and R. C. M. Simmen. 1998. Relationship between blood serum insulin-like growth factor 1 concentration and postweaning feed efficiency of crossbred cattle at three levels of dietary intake. J. Anim. Sci. 76:498-505.
55. Yang, J., S. H. Lee, M. E. Goodard, and P. M. Visscher. 2011. GCTA: A tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 88:76-82.