- Volume 27 Issue 9
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A Whole Genome Association Study on Meat Palatability in Hanwoo
- Hyeong, K.E. (School of Biotechnology, Yeungnam University) ;
- Lee, Y.M. (School of Biotechnology, Yeungnam University) ;
- Kim, Y.S. (School of Biotechnology, Yeungnam University) ;
- Nam, K.C. (Department of Animal Science and Technology, Sunchon National University) ;
- Jo, C. (Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Science, Seoul National University) ;
- Lee, K.H. (Department of Food and Nutrition, Korea National University of Transportation) ;
- Lee, J.E. (DNALink, Inc.) ;
- Kim, J.J. (School of Biotechnology, Yeungnam University)
- Received : 2014.04.08
- Accepted : 2014.07.21
- Published : 2014.09.01
A whole genome association (WGA) study was carried out to find quantitative trait loci (QTL) for sensory evaluation traits in Hanwoo. Carcass samples of 250 Hanwoo steers were collected from National Agricultural Cooperative Livestock Research Institute, Ansung, Gyeonggi province, Korea, between 2011 and 2012 and genotyped with the Affymetrix Bovine Axiom Array 640K single nucleotide polymorphism (SNP) chip. Among the SNPs in the chip, a total of 322,160 SNPs were chosen after quality control tests. After adjusting for the effects of age, slaughter-year-season, and polygenic effects using genome relationship matrix, the corrected phenotypes for the sensory evaluation measurements were regressed on each SNP using a simple linear regression additive based model. A total of 1,631 SNPs were detected for color, aroma, tenderness, juiciness and palatability at 0.1% comparison-wise level. Among the significant SNPs, the best set of 52 SNP markers were chosen using a forward regression procedure at 0.05 level, among which the sets of 8, 14, 11, 10, and 9 SNPs were determined for the respectively sensory evaluation traits. The sets of significant SNPs explained 18% to 31% of phenotypic variance. Three SNPs were pleiotropic, i.e. AX-26703353 and AX-26742891 that were located at 101 and 110 Mb of BTA6, respectively, influencing tenderness, juiciness and palatability, while AX-18624743 at 3 Mb of BTA10 affected tenderness and palatability. Our results suggest that some QTL for sensory measures are segregating in a Hanwoo steer population. Additional WGA studies on fatty acid and nutritional components as well as the sensory panels are in process to characterize genetic architecture of meat quality and palatability in Hanwoo.
Hanwoo;Single Nucleotide Polymorphism;Meat Quality;Palatability;Whole Genome Association
Supported by : Ministry of Agriculture, Forestry, and Fisheries
- Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. R. Ferreira, D. Bender, J. Maller, P. Sklar, P. I. W. de Bakker, M. J. Daly, and P. C. Sham. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81:559-575. https://doi.org/10.1086/519795
- Reardon, W., A. M. Mullen, T. Sweeney, and R. M. Hamill. 2010. Association of polymorphisms in candidate genes with colour, water- holding capacity, and composition traits in bovine M. longissimus and M. semimembranosus. Meat Sci. 86:270-275. https://doi.org/10.1016/j.meatsci.2010.04.013
- Rincon, G., K. L. Weber, A. L. Van Eenennaam, B. L. Golden, and J. F. Medrano. 2011. Hot topic: Performance of bovine high-density genotyping platforms in Holsteins and Jerseys. J. Dairy Sci. 94:6116-6121. https://doi.org/10.3168/jds.2011-4764
- Seaton G., C. S. Haley, S. A. Knott, M. Kearsey, and P. M. Visscher. 2002. QTL express: Mapping quantitative trait loci in simple and complex pedigree. Bioinformatics 18:339-340. https://doi.org/10.1093/bioinformatics/18.2.339
- Sturdivant, C. A., D. K. Lunt, G. C. Smith, and S. B. Smith. 1992. Fatty acid composition of subcutaneous and intramuscular adipose tissues and M. longissimusdorsi of Wagyu cattle. Meat Sci. 32:449-458. https://doi.org/10.1016/0309-1740(92)90086-J
- van Raden, P. M. 2008. Efficient methods to compute genomic predictions. J. Dairy Sci. 91:4414-4423. https://doi.org/10.3168/jds.2007-0980
- Waldman, R. C., G. G. Suess, and V. H. Brungardt. 1968. Fatty acids of certain bovine tissue and their association with growth, carcass and palatability traits. J. Anim. Sci. 27:632-635. https://doi.org/10.2527/jas1968.273632x
- Westerling, D. B. and H. B. Hedrick. 1979. Fatty acid composition of bovine lipids as influenced by diet, sex and anatomical location and relationship to sensory characteristics. J. Anim. Sci. 48:1343-1348. https://doi.org/10.2527/jas1979.4861343x
- Hartwell, L., L. Hood, M. L. Goldberg, L. M. Silver, and A. Reynolds. 2000. Genetics: from Genes to Genomes., McGraw-Hill College, Boston, MA, USA. 2nd ed. pp. 302-307.
- Jeremiah, L. E. 1996. The influence of subcutaneous fat thickness and marbling on beef: Palatability and consumer acceptability. Food Res. Int. 29:513-520. https://doi.org/10.1016/S0963-9969(96)00049-X
- Jo, C., S. H. Cho, J. Chang, and K. C. Nam. 2012. Keys to production and processing of Hanwoo beef: A perspective of tradition and science. Anim. Front. 2:32-38.
- Kim, Y., J. Ryu, J. Woo, J. B. Kim, C. Y. Kim, and C. Lee. 2011. Genome-wide association study reveals five nucleotide sequence variants for carcass traits in beef cattle. Anim. Genet. 42:361-365. https://doi.org/10.1111/j.1365-2052.2010.02156.x
- Lee, Y. M., C. M. Han, Y. Li, J. J. Lee, L. H. Kim, J. H. Kim, D. I. Kim, S. S. Lee, B. L. Park, H. D. Shin, K. S. Kim, N. S. Kim, and J. J. Kim. 2010. A whole genome association study to detect single nucleotide polymorphism for carcass traits in Hanwoo populations. Asian Australas. J. Anim. Sci. 23:417-424. https://doi.org/10.5713/ajas.2010.10019
- Lee, S. H., B. H. Choi, D. Lim, C. Gondro, Y. M. Cho, C. G. Dang, A. Sharma, G. W. Jang, K. T. Lee, D. Yoon, H. K. Lee, S. H. Yeon, B. S. Yang, H. S. Kang, and S. K. Hong. 2013. Genome-wide association study identifies major loci for carcass weight on BTA14 in Hanwoo (Korean cattle). PLoS ONE 8(10): e74677. https://doi.org/10.1371/journal.pone.0074677
- McKay, S. D., R. D. Schnabel, B. M. Murdoch, L. K. Matukumalli, J. Aerts, W. Coppieters, D. Crews, E. Dias Neto, C. A. Gill, C. Gao, H. Mannen, P. Stothard, Z. Wang, C. P. Van Tassell, J. L. Williams, J. F. Taylor, and S. S. Moore. 2007. Whole genome linkage disequilibrium maps in cattle. BMC Genet. 8:74.
- Melton, S. L., M. Amiri, G. W. Davis, and W. R. Backus. 1982. Flavor and chemical characteristics of ground beef from grass-, forage- grain- and grain-finished steers. J. Anim. Sci. 55:77-87. https://doi.org/10.2527/jas1982.55177x
- Decker, J. E., J. C. Pires, G. C. Conant, S. D. McKay, M. P. Heaton, K. Chen, A. Cooper, J. Vilkki, C. M. Seabury, A. R. Caetano, G. S. Johnson, R. A. Brenneman, O. Hanotte, L. S. Eggert, P. Wiener, J.-J. Kim, K. S. Kim, T. S. Sonstegard, C. van Tassell, H. L. Neibergs, J. C. McEwan, R. Brauning, L. L. Coutinho, M. E. Babar, G. A. Wilson, M. C. McClure, M. M. Rolf, J. Kim, R. D. Schnabel, and J. F. Taylor. 2009. Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proc. Natl. Acad. Sci. USA 106:18644-18649. https://doi.org/10.1073/pnas.0904691106
- Devlin, B. and N. Risch. 1995. A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 29:311-322. https://doi.org/10.1006/geno.1995.9003
- Dryden, F. D. and J. A. Maechello. 1970. Influence of total lipid and fatty acid composition upon the palatability of three bovine muscles. J. Anim. Sci. 31:36-41. https://doi.org/10.2527/jas1970.31136x
- Falconer, D. S. and T. F. C. Mackay. 1996. Introduction To Quantitative Genetics. 4th ed. Pearson/Prentice Hall, London, UK.
- Gill, J. L., S. C. Bishop, C. McCorquodale, J. L. Williams, and P. Wiener. 2009. Association of selected SNP with carcass and taste panel assessed meat quality traits in a commercial population of Aberdeen Angus-sired beef cattle. Genet. Sel. Evol. 41:36. https://doi.org/10.1186/1297-9686-41-36
- Gill, J. L., S. C. Bishop, C. McCorquodale, J. L. Williams, and P. Wiener. 2010. Associations between single nucleotide polymorphisms in multiple candidate genes and carcass and meat quality traits in a commercial Angus-cross population. Meat Sci. 86:985-993. https://doi.org/10.1016/j.meatsci.2010.08.005
- Goddard, M. E. and B. J. Hayes. 2009. Mapping genes for complex traits in domestic animals and their use in breeding programs. Nat. Rev. Genet. 10:381-391. https://doi.org/10.1038/nrg2575
- Gutierrez-Gil, B., P. Wiener, G. R. Nute, D. Burton, J. L. Gill, J. D. Wood, and J. L. Williams. 2008. Detection of quantitative trait loci for meat quality traits in cattle. Anim. Genet. 39:51-61. https://doi.org/10.1111/j.1365-2052.2007.01682.x
- Aulchenko, Y. S., D. J. de Koning, and C. Haley. 2007. Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics 177:577-585. https://doi.org/10.1534/genetics.107.075614
- Benjamini, Y. and Y. Hochberg. 1995. Controlling the false discovery rat: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B. 57:289-300.
- Berner, L. A. 1993. Defining the role of milk fat in balanced diets. Adv. Food Nutr. Res. 37:131-257. https://doi.org/10.1016/S1043-4526(08)60117-5
- Bonanome, A. and S. M. Grundy. 1988. Effect of dietary stearic acid on plasma cholesterol and lipoprotein levels. N. Engl. J. Med. 318:1244-1248. https://doi.org/10.1056/NEJM198805123181905
- Casas, E., J. W. Keele, S. D. Shackelford, M. Koohmaraie, T. S. Sonstegard, T. P. Smith, S. M. Kappes, and R. T. Stone. 1998. Association of the muscle hypertrophy locus with carcass traits in beef cattle. J. Anim. Sci. 76:468-473. https://doi.org/10.2527/1998.762468x
- 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. https://doi.org/10.2527/2003.81122976x
- 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. https://doi.org/10.2527/2000.783560x
- Choy, Y. H., B. H. Park, T. J. Choi, J. G. Choi, K. H. Cho, S. S. Lee, Y. L. Choi, K. C. Koh, and H. S. Kim. 2012. Estimation of relative economic weights of Hanwoo carcass traits based on carcass market price. Asian Australras. J. Anim. Sci. 25:1667-1673. https://doi.org/10.5713/ajas.2012.12397
- Churchill, G. A. and R. W. Doerge. 1994. Empirical threshold values for quantitative trait mapping. Genetics 138:963-971.
- Alam, M., Y. M. Lee, B. L. Park, J. H. Kim, S. S. Lee, H. D. Shin, K. S. Kim, N. S. Kim, and J. J. Kim. 2011. A whole genome association study to detect single nucleotide polymorphisms for body conformation traits in a Hanwoo population. Asian Australas. J. Anim. Sci. 24:322-329. https://doi.org/10.5713/ajas.2011.11012
Alexander, L. J., M. D. Macneil, T. W. Geary, W. M. Snelling, D. C. Rule, and J. A. Scanga. 2007. Quantitative trait loci with additive effects on palatability and fatty acid composition of meat in a Wagyu-Limousin
$F_2$population. Anim. Genet. 38:506-513. https://doi.org/10.1111/j.1365-2052.2007.01643.x
- Allais, S., H. Leveziel, 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. https://doi.org/10.2527/jas.2009-2385
Allais, S., L. Journaux, H. Leveziel, N. Payet-Duprat, P. Raynaud, J. F. Hocquette, J. Lepetit, S. Rousset, C. Denoyelle, C. Bernard-Capel, and G. Renand. 2011. Effects of polymorphisms in the calpastatin and
$\mu$-calpain genes on meat tenderness in 3 French beef breeds. J. Anim. Sci. 89:1-11. https://doi.org/10.2527/jas.2010-3063
- Genome-wide analysis of Hanwoo and Chikso populations using the BovineSNP50 genotyping array pp.2092-9293, 2018, https://doi.org/10.1007/s13258-018-0733-x