Genome-wide association analysis for quantitative trait loci influencing Warner-Bratzler shear force in five taurine cattle breeds

Animal Genetics

Volumn 43, Issue 6, 2012, Pages 662-673

  McClure, M C ^a,b   Ramey, H R ^a   Rolf, M M ^a   McKay, S D ^a   Decker, J E ^a   Chapple, R H ^a   Kim, J W ^a   Taxis, T M ^a   Weaber, R L ^a   Schnabel, R D ^a   Taylor, J F ^a  

^a UNIVERSITY OF MISSOURI   (United States)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

beef; Bos taurus taurus; calpain 1, (mu I) large subunit; calpastatin; genome wide association; haplotype; meat tenderness; quantitative trait loci; single nucleotide polymorphisms; Warner Bratzler shear force

Indexed keywords

CALCIUM BINDING PROTEIN; CALPAIN; CALPAIN 1; CALPASTATIN; CAPN1 PROTEIN, BOS TAURUS; MU-CALPAIN;

ANIMAL; ANIMAL DISEASE; ARTICLE; CATTLE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENETICS; GENOTYPE; MEAT; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CALCIUM-BINDING PROTEINS; CALPAIN; CATTLE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; MEAT; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

ANIMALIA; BOS; BOS TAURUS;

EID: 84867574316     PISSN: 02689146     EISSN: 13652052     Source Type: Journal    
DOI: 10.1111/j.1365-2052.2012.02323.x     Document Type: Article

References (59)

1. Alexander L.J., MacNeil M.D., Geary T.W., Snelling W.M., Rule D.C., &, Scanga J.A., (2007) Quantitative trait loci with additive effects on palatability and fatty acid composition of meat in a Wagyu-Limousin F2 population. Animal Genetics 38, 506-13. (Pubitemid 47480954)
2. Boleman S.J., Boleman S.L., Miller R.K., et al,. (1997) Consumer evaluation of beef of known categories of tenderness. Journal of Animal Science 75, 1521-4. (Pubitemid 127443298)
3. Casas E., Keele J.W., Shackelford S.D., Koohmaraie M., Sonstegard T.S., Smith T.P., Kappes S.M., &, Stone R.T., (1998) Association of the muscle hypertrophy locus with carcass traits in beef cattle. Journal of Animal Science 76, 468-73. (Pubitemid 128437889)
4. Casas E., Shackelford S.D., Keele J.W., Stone R.T., Kappes S.M., &, Koohmaraie M., (2000) Quantitative trait loci affecting growth and carcass composition of cattle segregating alternate forms of myostatin. Journal of Animal Science 78, 560-9.
5. Casas E., Stone R.T., Keele J.W., Shackelford S.D., Kappes S.M., &, Koohmaraie M., (2001) A comprehensive search for quantitative trait loci affecting growth and carcass composition of cattle segregating alternative forms of the myostatin gene. Journal of Animal Science 79, 854-60. (Pubitemid 33696100)
6. Casas E., Shackelford S.D., Keele J.W., Koohmaraie M., Smith T.P., &, Stone R.T., (2003) Detection of quantitative trait loci for growth and carcass composition in cattle. Journal of Animal Science 81, 2976-83. (Pubitemid 38571576)
7. Casas E., White S.N., Wheeler T.L., Shackelford S.D., Koohmaraie M., Riley D.G., Chase C.C. Jr, Johnson D.D., &, Smith T.P., (2006) Effects of calpastatin and micro-calpain markers in beef cattle on tenderness traits. Journal of Animal Science 84, 520-5. (Pubitemid 44405665)
8. Daetwyler H.D., Wiggans G.R., Hayes B.J., Woolliams J.A., &, Goddard M.E., (2011) Imputation of missing genotypes from sparse to high density using long-range phasing. Genetics 189, 317-27.
9. Davis G.P., Moore S.S., Drinkwater R.D., Shorthose W.R., Loxton I.D., Barendse W., &, Hetzel D.J., (2008) QTL for meat tenderness in the M. longissimus lumborum of cattle. Animal Genetics 39, 40-5. (Pubitemid 351178359)
10. Gill J.L., Bishop S.C., McCorquodale C., Williams J.L., &, Wiener P., (2009) Association of selected SNP with carcass and taste panel assessed meat quality traits in a commercial population of Aberdeen Angus-sired beef cattle. Genetics Selection Evolution 41, 36.
11. Gill J.L., Bishop S.C., McCorquodale C., Williams J.L., &, Wiener P., (2010) Associations between single nucleotide polymorphisms in multiple candidate genes and carcass and meat quality traits in a commercial Angus-cross population. Meat Science 86, 985-93.
12. Goll D.E., Thompson V.F., Li H., Wei W., &, Cong J., (2003) The calpain system. Physiological Reviews 83, 731-801. (Pubitemid 36828925)
13. Grobet L., Martin L.J., Poncelet D., et al,. (1997) A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle. Nature Genetics 17, 71-4. (Pubitemid 27377534)
14. Gutierrez-Gil B., Wiener P., Nute G.R., Burton D., Gill J.L., Wood J.D., &, Williams J.L., (2008) Detection of quantitative trait loci for meat quality traits in cattle. Animal Genetics 39, 51-61. (Pubitemid 351178363)
15. Habier D., Tetens J., Seefried F., Lichtner P., &, Thaller G., (2010) The impact of genetic relationship information on genomic breeding values in German Holstein cattle. Genetic Selection Evolution 425, 5.
16. Hayes B., &, Goddard M.E., (2001) The distribution of the effects of genes affecting quantitative traits in livestock. Genetics Selection Evolution 33, 209-29. (Pubitemid 32591810)
17. Huffman K.L., Miller M.F., Hoover L.C., Wu C.K., Brittin H.C., &, Ramsey C.B., (1996) Effect of beef tenderness on consumer satisfaction with steaks consumed in the home and restaurant. Journal of Animal Science 74, 91-7. (Pubitemid 126436692)
18. Johnston D.J., &, Graser H.U., (2010) Estimated gene frequencies of GeneSTAR markers and their size of effects on meat tenderness, marbling, and feed efficiency in temperate and tropical beef cattle breeds across a range of production systems. Journal of Animal Science 88, 1917-35.
19. 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, 910-5.
20. Keele J.W., Shackelford S.D., Kappes S.M., Koohmaraie M., &, Stone R.T., (1999) A region on bovine chromosome 15 influences beef longissimus tenderness in steers. Journal of Animal Science 77, 1364-71. (Pubitemid 129558828)
21. Kim N.-K., Lim D., Lee S.-H., Cho Y.-M., Park E.-W., Lee C.-S., Shin B.-S., Kim T.-H., &, Yoon D., (2011) Heat shock protein B1 and its regulator genes are negatively correlated with intramuscular fat content in the longissimus thoracis muscle of Hanwoo (Korean cattle) steers. Journal of Agricultural and Food Chemistry 59, 5657-64.
22. Kimura M., &, Ohta T., (1973) The age of a neutral mutant persisting in a finite population. Genetics 75, 199-212.
23. Lorenzen C.L., Hale D.S., Griffin D.B., Savell J.W., Belk K.E., Frederick T.L., Miller M.F., Montgomery T.H., &, Smith G.C., (1993) National Beef Quality Audit: survey of producer-related defects and carcass quality and quantity attributes. Journal of Animal Science 71, 1495-502.
24. Marchitelli C., Savarese M.C., Crisa A., Nardone A., Marsan P.A., &, Valentini A., (2003) Double muscling in Marchigiana beef breed is caused by a stop codon in the third exon of myostatin gene. Mammalian Genome 14, 392-5. (Pubitemid 36623546)
25. Matukumalli L.K., Lawley C.T., Schnabel R.D., et al,. (2009) Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE 4, e5350.
26. McKay S.D., Schnabel R.D., Murdoch B.M., et al,. (2007) Whole genome linkage disequilibrium maps in cattle. BMC Genetics 8, 74.
27. McKenna D.R., Roebert D.L., Bates P.K., et al,. (2002) National Beef Quality Audit-2000: survey of targeted cattle and carcass characteristics related to quality, quantity, and value of fed steers and heifers. Journal of Animal Science 80, 1212-22. (Pubitemid 41138436)
28. McPherron A.C., &, 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, 12457-61. (Pubitemid 27492550)
29. Meuwissen T.H., Hayes B.J., &, Goddard M.E., (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157, 1819-29. (Pubitemid 32298846)
30. Miller M.F., Huffman K.L., Gilbert S.Y., Hamman L.L., &, Ramsey C.B., (1995) Retail consumer acceptance of beef tenderized with calcium chloride. Journal of Animal Science 73, 2308-14.
31. Miller M.F., Carr M.A., Ramsey C.B., Crockett K.L., &, Hoover L.C., (2001) Consumer thresholds for establishing the value of beef tenderness. Journal of Animal Science 79, 3062-8. (Pubitemid 33721522)
32. Minick J.A., Dikeman M.E., Pollak E.J., &, Wilson D.E., (2004) Heritability and correlation estimates of Warner-Bratzler shear force and carcass traits from Angus-, Charolais-, Hereford, and Simmental-sired cattle. Canadian Journal of Animal Science 84, 599-609. (Pubitemid 40393864)
33. Mintert J., Lusk J.L., Schroeder T.C., Fox J.A., &, Koohmaraie M., (2000) Valuing beef tenderness. Technical Bulletin MF-2464. Kansas State University Agricultural Experiment Station and Cooperative Extension Service.
34. Morris C.A., Cullen N.G., Hickey S.M., Dobbie P.M., Veenvliet B.A., Manley T.R., Pitchford W.S., Kruk Z.A., Bottema C.D., &, Wilson T., (2006) Genotypic effects of calpain 1 and calpastatin on the tenderness of cooked M. longissimus dorsi steaks from Jersey × Limousin, Angus and Hereford-cross cattle. Animal Genetics 37, 411-4. (Pubitemid 44091675)
35. Moser D.W., Thallman R.M., Pollak E.J., Dikeman M.E., Gill C.A., Koontz S.R., Holm T.R., &, Dressler E.W., (2004) Meeting consumer demands through genetic selection: the NCBA Carcass Merit Project. Proceedings of the Beef Improvement Federation, pp. 42-4. Sioux Falls, South Dakota.
36. Page B.T., Casas E., Heaton M.P., et al,. (2002) Evaluation of single-nucleotide polymorphisms in CAPN1 for association with meat tenderness in cattle. Journal of Animal Science 80, 3077-85. (Pubitemid 41138346)
37. Page B.T., Casas E., Quaas R.L., et al,. (2004) Association of markers in the bovine CAPN1 gene with meat tenderness in large crossbred populations that sample influential industry sires. Journal of Animal Science 82, 3474-81. (Pubitemid 39584169)
38. Platter W.J., Tatum J.D., Belk K.E., Koontz S.R., Chapman P.L., &, Smith G.C., (2005) Effects of marbling and shear force on consumers' willingness to pay for beef strip loin steaks. Journal of Animal Science 83, 890-9.
39. Pryce J.E., Bolormaa S., Chamberlain A.J., Bowman P.J., Savin K., Goddard M.E., &, Hayes B.J., (2010) A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes. Journal of Dairy Science 93, 3331-45.
40. Reed D.R., Lawler M.P., &, Tordoff M.G., (2008) Reduced body weight is a common effect of gene knockout in mice. BMC Genetics 9, 4.
41. Rexroad C.E. 3rd, Bennett G.L., Stone R.T., Keele J.W., Fahrenkrug S.C., Freking B.A., Kappes S.M., &, Smith T.P., (2001) Comparative mapping of BTA15 and HSA11 including a region containing a QTL for meat tenderness. Mammalian Genome 12, 561-5. (Pubitemid 32552772)
42. Riley D.G., Chase C.C. Jr, Pringle T.D., West R.L., Johnson D.D., Olson T.A., Hammond A.C., &, Coleman S.W., (2003) Effect of sire on mu- and m-calpain activity and rate of tenderization as indicated by myofibril fragmentation indices of steaks from Brahman cattle. Journal of Animal Science 81, 2440-7. (Pubitemid 38571646)
43. Roeber D.L., Cannell R.C., Belk K.E., Tatum J.D., &, Smith G.C., (2000) Effects of a unique application of electrical stimulation on tenderness, color, and quality attributes of the beef longissimus muscle. Journal of Animal Science 78, 1504-9.
44. de Roos A.P.W., Hayes B.J., &, Goddard M.E., (2009) Reliability of genomic predictions across multiple populations. Genetics 183, 1545-53.
45. Sambrook J., Fritsch E.F., &, Maniatis T., (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Plainview, NY.
46. 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. American Journal of Human Genetics 78, 629-44.
47. Shook J.N., Vanoverbeke D.L., Scanga J.A., Belk K.E., Savell J.W., Lawrence T.E., Morgan J.B., Griffin D.B., Hale D.S., &, Smith G.C., (2008) The national Beef Quality Audit-2005, Phase 1: views of producers, packers, and merchandisers on current quality characteristics of the beef industry. The Professional Animal Scientist 24, 189-97.
48. Smith T.P., Casas E., Rexroad C.E. 3rd, Kappes S.M., &, Keele J.W., (2000) Bovine CAPN1 maps to a region of BTA29 containing a quantitative trait locus for meat tenderness. Journal of Animal Science 78, 2589-94.
49. Smith G.C., Savell J.W., Morgan J.B., &, Lawrence T.E., (2006) Report of the June-September 2005 national beef quality audit: A new benchmark for the U.S. beef industry. Proceedings of the Beef Improvement Federation, pp. 6-11. Mississippi State University, Choctaw, MS.
50. Stone R.T., Casas E., Smith T.P., Keele J.W., Harhay G., Bennett G.L., Koohmaraie M., Wheeler T.L., Shackelford S.D., &, Snelling W.M., (2005) 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 83, 2280-8.
51. Thallman R.M., Moser D.W., Dressler E.W., Totir R.L., Fernando R.L., Kachman S.D., Rumph J.M., Dikeman M.E., &, Pollak J.E., (2003) Carcass merit project: DNA marker validation Proc. Beef Improv. Fed. 8th Genet. Prediction Workshop 8: 70-90. Available at: http://www.beefimprovement.org/proceedings/ genetic-prediction-workshop/GPW-CarcassMeritProject-Final.pdf (accessed 10 May 2010).
52. The Bovine HapMap Consortium (2009) Genome wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324, 528-32.
53. Toosi A., Fernando R.L., &, Dekkers J.C.M., (2010) Genomic selection in admixed and crossbred populations. Journal of Animal Science 88, 32-46.
54. Van Eenennaam A.L., Li J., Thallman R.M., Quaas R.L., Dikeman M.E., Gill C.A., Franke D.E., &, Thomas M.G., (2007) Validation of commercial DNA tests for quantitative beef quality traits. Journal of Animal Science 85, 891-900. (Pubitemid 46651828)
55. VanRaden P.M., (2008) Efficient methods to compute genomic predictions. Journal of Dairy Science 91, 4414-23.
56. Weston A.R., Rogers R.W., &, Althen T.G., (2002) Review: The role of collagen in meat tenderness. The Professional Animal Scientist 18, 107-11.
57. Wheeler T.L., Shackelford S.D., &, Koohmaraie M., (1998) Cooking and palatability traits of beef longissimus steaks cooked with a belt grill or an open hearth electric broiler. Journal of Animal Science 76, 2805-10. (Pubitemid 128464886)
58. White S.N., Casas E., Wheeler T.L., Shackelford S.D., Koohmaraie M., Riley D.G., Chase C.C. Jr, Johnson D.D., Keele J.W., &, Smith T.P., (2005) A new single nucleotide polymorphism in CAPN1 extends the current tenderness marker test to include cattle of Bos indicus, Bos taurus, and crossbred descent. Journal of Animal Science 83, 2001-8.
59. Zimin A.V., Delcher A.L., Florea L., et al,. (2009) A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology 10, R42.