Association analysis for feed efficiency traits in beef cattle using preserved haplotypes

Genome

Volumn 56, Issue 10, 2013, Pages 586-591

  Lu, Duc ^a,b   Sargolzaei, Mehdi ^a   Li, Changxi ^b,c   Abo Ismail, Mohammed ^a,d   Vander Voort, Gordon ^a   Wang, Zhiquan ^b   Plastow, Graham ^b   Moore, Stephen ^e   Miller, Stephen P ^a  

^a UNIVERSITY OF GUELPH   (Canada)

^b UNIVERSITY OF ALBERTA   (Canada)

^c LACOMBE RESEARCH CENTRE   (Canada)

^d DAMANHOUR UNIVERSITY   (Egypt)

^e UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Association; Beef cattle; Feed efficiency; Haplotype

Indexed keywords

ANIMAL; ANIMAL FOOD; ARTICLE; CATTLE; CHROMOSOME; EATING; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENETICS; GENOME; GENOTYPE; HAPLOTYPE; PHENOTYPE; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; WEIGHT GAIN;

ANIMAL FEED; ANIMALS; CATTLE; CHROMOSOMES, MAMMALIAN; EATING; GENETIC ASSOCIATION STUDIES; GENETIC VARIATION; GENOME; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HAPLOTYPES; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; WEIGHT GAIN;

EID: 84889841325     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/gen-2013-0072     Document Type: Article

References (48)

1. Akey J. Jin L. Xiong M. 2001. Haplotypes vs. single marker linkage disequilibrium tests: what do we gain? Eur. J. Hum. Genet. 9: 291-300. 10.1038/sj.ejhg.5200619. 11313774. (Pubitemid 32366698)
2. Alberta Agriculture and Rural Development. 2006. Residual feed intake (net feed efficiency) in beef cattle. [Online.] Available from http://www1.agric.gov.ab.ca/$department/deptdocs.nsf/all/agdex10861 [accessed 10 January 2013].
3. 2 population. Anim. Genet. 38 (4): 413-416. 10.1111/j.1365-2052.2007.01616.x. 17596127. (Pubitemid 47106718)
4. Arthur P.F. Archer J.A. Johnston D.J. Herd R.M. Richardson E.C. Parnell P.F. 2001 a. Genetic and phenotypic variance and covariance components for feed intake, feed efficiency, and other postweaning traits in Angus cattle. J. Anim. Sci. 79: 2805-2811. 11768108. (Pubitemid 33721430)
5. Arthur P.F. Renand G. Krauss D. 2001 b. Genetic and phenotypic relationships among different measures of growth and feed efficiency in young Charolais bulls. Livest. Prod. Sci. 68: 131-139. 10.1016/S0301-6226(00)00243-8. (Pubitemid 32224559)
6. Ben Jemaa S. Fritz S. Guillaume F. Druet T. Denis C. Eggen A. Gautier M. 2008. Detection of quantitative trait loci affecting non-return rate in French dairy cattle. J. Anim. Breed. Genet. 125 (4): 280-288. 10.1111/j.1439-0388.2008. 00744.x. 18717969. (Pubitemid 352019654)
7. Benjamini Y. Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B, 57: 289-300.
8. Boichard D. Grohs C. Bourgeois F. Cerqueira F. Faugeras R. Neau A. et al 2003. Detection of genes influencing economic traits in three French dairy cattle breeds. Genet. Sel. Evol. 35 (1): 77-101. 10.1186/1297-9686-35-1-77. 12605852. (Pubitemid 36530731)
9. Casas E. Shackelford S.D. Keele J.W. Koohmaraie M. Smith T.P.L. Stone R.T. 2003. Detection of quantitative trait loci for growth and carcass composition in cattle. J. Anim. Sci. 81: 2976-2983. 14677852. (Pubitemid 38571576)
10. Crews, D.H., Moore, S.S., and Enns, R.M. 2008. Optimizing traditional and marker assisted evaluation in beef cattle. In Proceedings of the 40th Beef Improvement Federation, Calgary, Alberta. pp. 44-49.
11. Druet T. Fritz S. Sellem E. Basso B. Gérard O. Salas-Cortes L. et al 2009. Estimation of genetic parameters and genome scan for 15 semen characteristics traits of Holstein bulls. J. Anim. Breed. Genet. 126 (4): 269-277. 10.1111/j.1439-0388.2008.00788.x. 19630877.
12. Dunner S. Checa M.L. Gutierrez J.P. Martin J.P. Cañon J. 1998. Genetic analysis and management in small populations: the asturcon pony as an example. Genet. Sel. Evol. 30: 397-405. 10.1186/1297-9686-30-4-397. (Pubitemid 28527611)
13. Gabriel S.B. Schaffner S.F. Nguyen H. Moore J.M. Roy J. Blumenstiel B. et al 2002. The structure of haplotype blocks in the human genome. Science, 296 (5576): 2225-2229. 10.1126/science.1069424. 12029063. (Pubitemid 34680308)
14. Gilmour, A.R., Gogel, B.J., Cullis, B.R., and Thompson, R. 2009. ASReml user guide release 3.0. Available from http://vsni.de/downloads/asreml/release3/ UserGuide.pdf.
15. Grandin, T., and Deesing, M.J. 1998. Genetics and behavior during handling, restraint and herding. In Genetics and the behavior of domestic animals. Edited by T. Grandin. Academic Press, San Diego, Calif. pp. 113-144.
16. Groeneveld, E., Kovac, M., and Mielenz, N. 2008. VCE user's guide and reference manual, Version 6.0. Institute of Farm Animal Genetics, Mariensee, Germany. Available from ftp://ftp.tzv.fal.de/pub/vce6/doc/vce6-manual-3.1-A4. pdf.
17. Gutiérrez-Gil B. Ball N. Burton D. Haskell M. Williams J.L. Wiener P. 2008. Identification of quantitative trait loci affecting cattle temperament. J. Hered. 99 (6): 629-638. 10.1093/jhered/esn060. 18784067.
18. Gutiérrez-Gil B. Williams J.L. Homer D. Burton D. Haley C.S. Wiener P. 2009. Search for quantitative trait loci affecting growth and carcass traits in a cross population of beef and dairy cattle. J. Anim. Sci. 87 (1): 24-36. 18791160.
19. Hanotte O. Ronin Y. Agaba M. Nilsson P. Gelhaus A. Horstmann R. 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. Proc. Natl. Acad. Sci. U.S.A. 100 (13): 7443-7448. 10.1073/pnas. 1232392100. 12805560. (Pubitemid 36759988)
20. Herd R.M. Arthur P.F. 2009. Physiological basis for residual feed intake. J. Anim. Sci. 87: E64-E71. 10.2527/jas.2008-1345. 19028857.
21. Herd R.M. Bishop S.C. 2000. Genetic variation in residual feed intake and its association with other production traits in British Hereford cattle. Livest. Prod. Sci. 63: 111-119. 10.1016/S0301-6226(99)00122-0. (Pubitemid 30231201)
22. Höglund J.K. Guldbrandtsen B. Su G. Thomsen B. Lund M.S. 2009. Genome scan detects quantitative trait loci affecting female fertility traits in Danish and Swedish Holstein cattle. J. Dairy Sci. 92 (5): 2136-2143. 10.3168/jds.2008-1104. 19389971.
23. Holmberg M. Andersson-Eklund L. 2006. Quantitative trait loci affecting fertility and calving traits in Swedish dairy cattle. J. Dairy Sci. 9 (89): 3664-3671. 10.3168/jds.S0022-0302(06)72406-7. (Pubitemid 44306012)
24. Hoque M.A. Oikawa T. 2004. Comparison and relation among different estimates of residual feed intake for Japanese Black (Wagyu) bulls. J. Anim. Sci. 75: 201-205. 10.1111/j.1740-0929.2004.00176.x. (Pubitemid 38865789)
25. Imumorin I.G. Kim E.-H. Lee Y.-M. De Koning D.-J. van Arendonk J.A. De Donato M. et al 2011. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits. Front. Genet. 2: 44. 22303340.
26. +/- mouse, a model of Cornelia de Lange Syndrome. PLoS Genet. 5 (9): e1000650. 10.1371/journal.pgen.1000650. 19763162.
27. 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. J. Anim. Sci. 81: 1933-1942. 12926775. (Pubitemid 38571708)
28. Kühn Ch. Bennewitz J. Reinsch N. Xu N. Thomsen H. Looft C. et al 2003. Quantitative trait loci mapping of functional traits in the German Holstein cattle population. J. Dairy Sci. 86 (1): 360-368. 10.3168/jds.S0022- 0302(03)73614-5. 12613879. (Pubitemid 39067189)
29. Li C. Basarab J. Snelling W.M. Benkel B. Murdoch B. Hansen C. Moore S.S. 2004. Assessment of positional candidate genes myf5 and igf1 for growth on bovine chromosome 5 in commercial lines of Bos taurus. J. Anim. Sci. 82: 1-7. 14753343. (Pubitemid 38572399)
30. Li F. Chen H. Lei C.Z. Ren G. Wang J. Li Z.J. Wang J.Q. 2010. Novel SNPs of the bovine NUCB2 gene and their association with growth traits in three native Chinese cattle breeds. Mol. Biol. Rep. 37 (1): 541-546. 10.1007/s11033-009-9732-y. 19728157.
31. Lush J.L. 1951. The impact of genetics and animal breeding. J. Anim. Sci. 10: 311-321. 14832132.
32. McClure M.C. Morsci N.S. Schnabel R.D. Kim J.W. Yao P. Rolf M.M. et al 2010. A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle. Anim. Genet. 41 (6): 597-607. 10.1111/j.1365-2052.2010.02063.x. 20477797.
33. Moore S.S. Mujibi F.D. Sherman E.L. 2009. Molecular basis for residual feed intake in beef cattle. J. Anim. Sci. 87: E41-E47. 10.2527/jas.2008-1418. 18952728.
34. Morris R.W. Kaplan N.L. 2002. On the advantage of haplotype analysis in the presence of multiple disease susceptibility alleles. Genet. Epidemiol. 23: 221-233. 10.1002/gepi.10200. 12384975.
35. Nalaila S.M. Stothard P. Moore S.S. Li C. Wang Z. 2012. Whole-genome QTL scan for ultrasound and carcass merit traits in beef cattle using Bayesian shrinkage method. J. Anim. Breed. Genet. 129 (2): 107-119. 10.1111/j.1439-0388. 2011.00954.x. 22394233.
36. Neumaier A. Groeneveld E. 1998. Restricted maximum likelihood estimation of covariances in sparse linear models. Genet. Sel. Evol. 1 (30): 3-26. 10.1186/1297-9686-30-1-3. (Pubitemid 28169219)
37. Nkrumah J.D. Sherman E.L. Li C. Marques E. Crews D.H. Bartusiak R. Jr. et al 2007. Primary genome scan to identify putative quantitative trait loci for feedlot growth rate, feed intake, and feed efficiency of beef cattle. J. Anim. Sci. 85 (12): 3170-3181. 10.2527/jas.2007-0234. (Pubitemid 350247368)
38. O'Blesness G.V. Van Vleck L.D. Henderson C.R. 1960. Heritabilities of some type appraisal traits and their genetic and phenotypic correlations with production. J. Dairy Sci. 42: 1490-1498. 10.3168/jds.S0022-0302(60)90354-4.
39. Purcell S. Neale B. Todd-Brown K. Thomas L. Ferreira M.A. Bender D. et al 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81 (3): 559-575. 10.1086/519795. 17701901. (Pubitemid 47330214)
40. Sabeti P.C. Reich D.E. Higgins J.M. Levine H.Z.P. Richter D.J. Schaffner S.F. et al 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature, 419: 832-837. 10.1038/nature01140. 12397357. (Pubitemid 35238568)
41. Scheet P. Stephens M. 2006. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am. J. Hum. Genet. 78: 629-644. 10.1086/502802. 16532393.
42. Schrooten C. Bink M.C.A.M. Bovenhuis H. 2004. Whole genome scan to detect chromosomal regions affecting multiple traits in dairy cattle. J. Dairy Sci. 87 (10): 3550-3560. 10.3168/jds.S0022-0302(04)73492-X. 15377635. (Pubitemid 39408491)
43. Sherman E.L. Nkrumah J. D Murdoch B.M. Moore S.S. 2008. Identification of polymorphisms influencing feed intake and efficiency in beef cattle. Anim. Genet. 39 (3): 225-231. 10.1111/j.1365-2052.2008.01704.x.
44. Sherman E.L. Nkrumah J.D. Li C. Bartusiak R. Murdoch B. Moore S.S. 2009. Fine mapping quantitative trait loci for feed intake and feed efficiency in beef cattle. J. Anim. Sci. 87 (1): 37-45. 10.2527/jas.2008-0876. 18791150.
45. Shrode R.R. Hammack S.P. 1971. Chute behavior of yearling beef cattle. J. Anim. Sci. 33: 193. [Abstract.]
46. Stricklin W.R. Heisler C.E. Wilson L.L. 1980. Heritability of temperament in beef cattle. J. Anim. Sci. 51 (Suppl. 1): 109. [Abstract.]
47. Takasuga A. Watanabe T. Mizoguchi Y. Hirano T. Ihara N. Takano A. et al 2007. Identification of bovine QTL for growth and carcass traits in Japanese Black cattle by replication and identical-by-descent mapping. Mamm. Genome, 18 (2): 125-136. 10.1007/s00335-006-0096-5. (Pubitemid 46425384)
48. Zimin A.V. Delcher A.L. Florea L. Kelley D.R. Schatz M.C. Puiu D. et al 2009. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol. 10 (4): R42. 10.1186/gb-2009-10-4-r42. 19393038.