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Genetic association of marbling score with intragenic nucleotide variants at selection signals of the bovine genome

  • J. Ryu (a1) and C. Lee (a1)


Selection signals of Korean cattle might be attributed largely to artificial selection for meat quality. Rapidly increased intragenic markers of newly annotated genes in the bovine genome would help overcome limited findings of genetic markers associated with meat quality at the selection signals in a previous study. The present study examined genetic associations of marbling score (MS) with intragenic nucleotide variants at selection signals of Korean cattle. A total of 39 092 nucleotide variants of 407 Korean cattle were utilized in the association analysis. A total of 129 variants were selected within newly annotated genes in the bovine genome. Their genetic associations were analyzed using the mixed model with random polygenic effects based on identical-by-state genetic relationships among animals in order to control for spurious associations produced by population structure. Genetic associations of MS were found (P<3.88×10−4) with six intragenic nucleotide variants on bovine autosomes 3 (cache domain containing 1, CACHD1), 5 (like-glycosyltransferase, LARGE), 16 (cell division cycle 42 binding protein kinase alpha, CDC42BPA) and 21 (snurportin 1, SNUPN; protein tyrosine phosphatase, non-receptor type 9, PTPN9; chondroitin sulfate proteoglycan 4, CSPG4). In particular, the genetic associations with CDC42BPA and LARGE were confirmed using an independent data set of Korean cattle. The results implied that allele frequencies of functional variants and their proximity variants have been augmented by directional selection for greater MS and remain selection signals in the bovine genome. Further studies of fine mapping would be useful to incorporate favorable alleles in marker-assisted selection for MS of Korean cattle.


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Barresi, R, Michele, DE, Kanagawa, M, Harper, HA, Dovico, SA, Satz, JS, Moore, SA, Zhang, W, Schachter, H, Dumanski, JP, Cohn, RD, Nishino, I and Campbell, KP 2004. LARGE can functionally bypass α-dystroglycan glycosylation defects in distinct congenital muscular dystrophies. Nature Medicine 10, 696703.
Kanagawa, M, Saito, F, Kunz, S, Yoshida-Moriguchi, T, Barresi, R, Kobayashi, YM, Muschler, J, Dumanski, JP, Michele, DE, Oldstone, MB and Campbell, KP 2004. Molecular recognition by LARGE is essential for expression of functional dystroglycan. Cell 117, 953964.
Kang, HM, Sul, JH, Service, SK, Zaitlen, NA, Kong, SY, Freimer, NB, Sabatti, C and Eskin, E 2010. Variance component model to account for sample structure in genome-wide association studies. Nature Genetics 42, 348354.
Kim, JB and Lee, C 2000. Historical look at the genetic improvement in Korean cattle. Asian-Australasian Journal of Animal Sciences 13, 14671481.
Kim, Y, Ryu, J, Woo, J, Kim, JB, Kim, CY and Lee, C 2011. Genome-wide association study reveals five nucleotide sequence variants for carcass traits in beef cattle. Animal Genetics 42, 361365.
Lee, C and Pollak, EJ 2002. Genetic antagonism between body weight and milk production in beef cattle. Journal of Animal Science 80, 316321.
Lee, Y, Oh, D, Lee, J, La, B and Yeo, J 2013. Novel single nucleotide polymorphisms of bovine SREBP1 gene is association with fatty acid composition and marbling score in commercial Korean cattle (Hanwoo). Molecular Biology Reports 40, 247254.
Ponsuksili, S, Murani, E, Phatsara, C, Schwerin, M, Schellander, K and Wimmers, K 2009. Porcine muscle sensory attributes associate with major changes in gene networks involving CAPZB, ANKRD1, and CTBP2. Functional & Integrative Genomics 9, 455471.
Ryoo, H and Lee, C 2014. Underestimation of heritability using a mixed model with a polygenic covariance structure in a genome-wide association study for complex traits. European Journal of Human Genetics 22, 851854.
Ryu, J, Kim, Y, Kim, C, Kim, J and Lee, C 2012. Association of bovine carcass phenotypes with genes in an adaptive thermogenesis pathway. Molecular Biology Reports 39, 14411445.
Ryu, J and Lee, C 2014. Identification of contemporary selection signatures using composite log likelihood and their associations with marbling score in Korean cattle. Animal Genetics 45, 765770.
Shin, J and Lee, C 2015a. Statistical power for identifying nucleotide markers associated with quantitative traits in genome-wide association analysis using a mixed model. Genomics 105, 14.
Shin, J and Lee, C 2015b. A mixed model reduces spurious genetic associations produced by population stratification in genome-wide association studies. Genomics 105, 191196.
Yang, J, Lee, SH, Goddard, ME and Visscher, PM 2011. GCTA: a tool for genome-wide complex trait analysis. American Journal of Human Genetics 88, 7682.
Zhang, Z, Ersoz, E, Lai, CQ, Todhunter, RJ, Tiwari, HK, Gore, MA, Bradbury, PJ, Yu, J, Arnett, DK, Ordovas, JM and Buckler, ES 2010. Mixed linear model approach adapted for genome-wide association studies. Nature Genetics 42, 355360.
Zhao, X, Liu, ZY and Liu, QX 2015. Gene coexpression networks reveal key drivers of phenotypic divergence in porcine muscle. BMC Genomics 16, 50.



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