Browse > Article
http://dx.doi.org/10.5713/ajas.15.0752

Genome-wide Association Study to Identify Quantitative Trait Loci for Meat and Carcass Quality Traits in Berkshire  

Iqbal, Asif (School of Biotechnology, Yeungnam University)
Kim, You-Sam (School of Biotechnology, Yeungnam University)
Kang, Jun-Mo (School of Biotechnology, Yeungnam University)
Lee, Yun-Mi (School of Biotechnology, Yeungnam University)
Rai, Rajani (School of Biotechnology, Yeungnam University)
Jung, Jong-Hyun (Jung P&C Institute)
Oh, Dong-Yup (Livestock Research Institute)
Nam, Ki-Chang (Department of Animal Science and Technology, Sunchon National University)
Lee, Hak-Kyo (Department of Animal Biotechnology, Chonbuk National University)
Kim, Jong-Joo (School of Biotechnology, Yeungnam University)
Publication Information
Asian-Australasian Journal of Animal Sciences / v.28, no.11, 2015 , pp. 1537-1544 More about this Journal
Abstract
Meat and carcass quality attributes are of crucial importance influencing consumer preference and profitability in the pork industry. A set of 400 Berkshire pigs were collected from Dasan breeding farm, Namwon, Chonbuk province, Korea that were born between 2012 and 2013. To perform genome wide association studies (GWAS), eleven meat and carcass quality traits were considered, including carcass weight, backfat thickness, pH value after 24 hours (pH24), Commission Internationale de l'Eclairage lightness in meat color (CIE L), redness in meat color (CIE a), yellowness in meat color (CIE b), filtering, drip loss, heat loss, shear force and marbling score. All of the 400 animals were genotyped with the Porcine 62K SNP BeadChips (Illumina Inc., USA). A SAS general linear model procedure (SAS version 9.2) was used to pre-adjust the animal phenotypes before GWAS with sire and sex effects as fixed effects and slaughter age as a covariate. After fitting the fixed and covariate factors in the model, the residuals of the phenotype regressed on additive effects of each single nucleotide polymorphism (SNP) under a linear regression model (PLINK version 1.07). The significant SNPs after permutation testing at a chromosome-wise level were subjected to stepwise regression analysis to determine the best set of SNP markers. A total of 55 significant (p<0.05) SNPs or quantitative trait loci (QTL) were detected on various chromosomes. The QTLs explained from 5.06% to 8.28% of the total phenotypic variation of the traits. Some QTLs with pleiotropic effect were also identified. A pair of significant QTL for pH24 was also found to affect both CIE L and drip loss percentage. The significant QTL after characterization of the functional candidate genes on the QTL or around the QTL region may be effectively and efficiently used in marker assisted selection to achieve enhanced genetic improvement of the trait considered.
Keywords
Genome Wide Association Study; Berkshire; Quantitative Trait Loci; Single Nucleotide Polymorphism; Meat Quality;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Bonneau, M. and B. Lebret. 2010. Production systems and influence on eating quality of pork. Meat Sci. 84:293-300.   DOI   ScienceOn
2 Davoli, R. and S. Braglia. 2007. Molecular approaches in pig breeding to improve meat quality. Brief. Funct. Genomic. Proteomic. 6:313-321.
3 Edwards, D. B., C. W. Ernst, N. E. Raney, M. E. Doumit, M. D. Hoge, and R. O. Bates. 2008. Quantitative trait locus mapping in an F2 Duroc$\times$Pietrain resource population: II. Carcass and meat quality traits. J. Anim. Sci. 86:254-266.   DOI
4 Evans, G. J., E. Giuffra, A. Sanchez, S. Kerje, G. Davalos, O. Vidal, S. Illan, J. L. Noguera, L. Varona, I. Velander, O. I. SouthwoodI, D. J, de Koning, C. S. Haley, G. S. Plastow, and L. Andersson. 2004. Identification of quantitative trait loci for production traits in commercial pig populations. Genetics 164: 621-627.
5 Falconer, D. S. and T. F. C. Mackay. 2006. Introduction to Quantitative Genetics. 4th ed. Longman Group Ltd., Essex, England.
6 Feng, Z. M., X. Zhou, H. Shao, X. F. Kong, Y. L. Yin, and R. Huang. 2012. Genotyping of five Chinese local pig breeds focused on meat quality by using PCR-RFLP based on halothane and Mx1. J. Food Agric. Environ. 10(3&4):840-845.
7 Fontanesi, L., G. Schiavo, G. Galimberti, D. G. Calo, E. Scotti, P. L. Martelli, L. Buttazzoni, R. Casadio, and V. Russo. 2012. A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes. BMC Genomics 13:583.   DOI
8 Fowler, K. E., R. Pong-Wong, J. Bauer, E. J. Clemente, C. P. Reitter, N. A. Affara, S. Waite, G. A. Walling, and D. K. Griffin. 2013. Genome wide analysis reveals single nucleotide polymorphisms associated with fatness and putative novel copy number variants in three pig breeds. BMC Genomics 14:784.   DOI   ScienceOn
9 Goddard, M. E. and B. J. Hayes. 2009. Mapping genes for complex traits in domestic animals and their use in breeding programmes Nat. Rev. Genet. 10: 381-391.   DOI   ScienceOn
10 Goodwin, R. and S. Burroughs. 1995. Genetic Evaluation Terminal Line Program Results. National Pork Producers Council, Des Moines, IA, USA.
11 Jeffrey J. W. and S. P. Randall. 2011. Genetic modifications of pigs for medicine and agriculture. Mol. Reprod. Dev. 78:879-891.   DOI   ScienceOn
12 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, S. H. Lee, H. K. 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.   DOI   ScienceOn
13 Li, H. D., M. S. Lund, O. F. Christensen, V. R. Gregersen, P. Henckel and C. Bendixen. 2010. Qunatitative trait loci analysis of swine meat quality traits. J. Anim. Sci. 88:2904-2912.   DOI   ScienceOn
14 Meuwissen, T. H. E., B. J. Hayes, and M. E. Goddard. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819-1829.
15 Liu, G., D. G. J. Jennen, E. Tholen, H. Juengst, T. Kleinwachter, M. Holker, D. Tesfaye, G. Un, H. J. Schreinemachers, E. Murani, S. Ponsuksili, J. J. Kim, K. Schellander, and K. Wimmers. 2007. A genome scan reveals QTL for growth, fatness, leanness and meat quality in a Duroc-Pietrain resource population. Anim. Genet. 38:241-252.   DOI   ScienceOn
16 Luo, W., S. Chen, D. Cheng, L. Wang, Y. Li, X. Ma, X. Song, X. Liu, W. Li, J. Liang, H. Yan, K. Zhao, C. Wang, L. Wang, and L. Zhang. 2012. Genome-wide association study of porcine hematological parameters in a large White $\times$ Minzhu F2 resource population. Int. J. Biol. Sci. 8:870-881.   DOI
17 Ma, J., J. Ren, Y. Guo, Y. Duan, N. Ding, L. Zhou, L. Li, X. Yan, K. Yang, L. Huang, Y. Song, J. Xie, D. Milan, and L. Huang. 2009. Genome-wide identification of quantitative trait loci for carcass composition and meat quality in a large-scale White Duroc$\times$Chinese Erhualian resource population. Anim. Genet. 40:637-647.   DOI   ScienceOn
18 Neter, J., W. Wasserman, and M. H. Kutner. 1990. Applied linear statistical models. 3rd ed. Irwin, Boston, MA, USA.
19 NPPC. 2000. Pork composition and quality assessment procedures. National Pork Producers Council, Des Moines, IA, USA.
20 Pierzchala, M., D. Cieslak, G. Reiner, H. Bartenschlager, G. Moser, and H. Geldermann. 2003. Linkage and QTL mapping for Sus scrofa chromosome 17. J. Anim. Breed. Genet. 120:132-137.
21 Ponsuksili, S., E. Murani, N. Trakooljul, M. Schwerin, and K. Wimmers. 2014. Discovery of candidate genes for muscle traits based on GWAS supported by eQTL-analysis. Int. J. Biol. Sci. 10:327-337.   DOI   ScienceOn
22 Rothschild, M. F. and A. Ruvinsky. 2011. The Genetics of the Pig CABI 2nd ed., Oxfordshire, UK.
23 Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. Ferreira, D. Bender, J. Maller, P. Sklar, P. I. 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.   DOI   ScienceOn
24 Rambow F., G. Piton, S. Bouet, J. J. Leplat, S. Baulande, A. Marrau, M. Stam, V. Horak, and V. N. Silvia. 2008. Gene expression signature for spontaneous cancer regression in melanoma pigs. Neoplasia 10:714-726.   DOI
25 Rohrer, G. A., R. M. Thallman, S. Shackelford, T. Wheeler, and M. Koohmaraie. 2006. A genome scan for loci affecting pork quality in a Duroc-Landrace F2 population. Anim. Genet. 37: 17-27.   DOI   ScienceOn
26 Sanchez, M. P., T. Tribout, N. Iannuccelli, M. Bouffaud, B. Servin, A. Tenghe, P. Dehais, N. Muller, M. P. D. Schneider, M. J. Mercat, C. Rogel-Gaillard, D. Milan, J. P. Bidanel, and H. Gilbert. 2014. A genome-wide association study of production traits in a commercial population of Large White pigs: evidence of haplotypes affecting meat quality. Genet. Sel. Evol. 46:12.   DOI   ScienceOn
27 Suzuki, K., M. Irie, H. Kadowaki, T. Shibata, M. Kumagai, and A. Nishida. 2005. Genetic parameter estimates of meat quality traits in Duroc pigs selected for average daily gain, longissimus muscle area, backfat thickness, and intramuscular fat content. J. Anim. Sci. 83:2058-2065.   DOI
28 Van Wijk, H. J., H. Buschbell, B. Dibbits, S. C. Liefers, B. Harlizius, H. C. M. Heuven, E. F. Knol, H. Bovenhuis, and M. A. M. Groenen. 2007. Variance component analysis of quantitative trait loci for pork carcass composition and meat quality on SSC4 and SSC11. J. Anim. Sci. 85:22-30.   DOI   ScienceOn
29 Yue, G., A. Stratil, M. Kopecny, D. Schroffelova, Jr. J. Schroffel, J. Hojny, S. Cepica, R. Davoli, P. Zambonelli, C. Brunsch, I. Sternstein, G. Moser, H. Bartenschlager, G. Reiner, and H. Geldermann. 2003. Linkage and QTL mapping for Sus scrofa chromosome 6. J. Anim. Breed. Genet. 120:45-55.   DOI   ScienceOn