Korean Journal of Agricultural Science (농업과학연구)

Institute of Agricultural Science, CNU (충남대학교 농업과학연구소)
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Genome-wide association study identifies positional candidate genes affecting back fat thickness trait in pigs

  • Lee, Jae-Bong (Korea Zoonosis Research Institute (KoZRI), Chonbuk National University) ;
  • Kang, Ho-Chan (Division of Applied Life Science (BK21 plus), Gyeongsang National University) ;
  • Kim, Eun-Ho (Division of Applied Life Science (BK21 plus), Gyeongsang National University) ;
  • Kim, Yoon-Joo (Division of Applied Life Science (BK21 plus), Gyeongsang National University) ;
  • Yoo, Chae-Kyoung (Institute of Agriculture and Life Science, Gyeongsang National University) ;
  • Choi, Tae-Jeong (Swine Science Division, National Institute of Animal Science, RDA) ;
  • Lim, Hyun-Tae (Division of Applied Life Science (BK21 plus), Gyeongsang National University)
  • Received : 2018.05.04
  • Accepted : 2018.07.24
  • Published : 2018.12.31
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Abstract

This study was done to search for positional candidate genes associated with the back fat thickness trait using a Genome-Wide Association Study (GWAS) in purebred Yorkshires (N = 1755). Genotype and phenotype analyses were done for 1,642 samples. As a result of the associations with back fat thickness using the Gemma program (ver. 0.93), when the genome-wide suggestive threshold was determined using the Bonferroni method ($p=1.61{\times}10^{-5}$), the single nucleotide polymorphism (SNP) markers with suggestive significance were identified in 1 SNP marker on chromosome 2 (MARC0053928; $p=3.65{\times}10^{-6}$), 2 SNP markers on chromosome 14 (ALGA0083078; $p=7.85{\times}10^{-6}$, INRA0048453; $p=1.27{\times}10^{-5}$), and 1 SNP marker on chromosome 18 (ALGA0120564; $p=1.44{\times}10^{-5}$). We could select positional candidate genes (KCNQ1, DOCK1, LOC106506151, and LOC110257583), located close to the SNP markers. Among these, we identified a potassium voltage-gated channel subfamily Q member gene (KCNQ1) and the dedicator of cytokinesis 1 (DOCK1) gene associated with obesity and Type-2 diabetes. The SNPs and haplotypes of the KCNQ1 and DOCK1 genes can contribute to understanding the genetic structure of back fat thickness. Additionally, it may provide basic data regarding marker assisted selection for a meat quality trait in pigs.

Keywords

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Fig. 1. Manhattan plots (A) and quantile-quantile plots (B) of the GWAS for back fat thickness. The x-axis shows the physical positions of the SNP markers on the pig chromosomes and the association signal on the y-axis (shown as - log10p). The Manhattan plots show the identification for back fat thickness trait on SSC2, 14, 18. GWAS, Genome-Wide Association Study; SNP, Single Nucleotide Polymorphism; SSC, Sus scrofa chromosome.

Table 1. Descriptive statistics of back fat thickness trait in Yorkshire.

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Table 2. Genome-wide association analysis results of SNP markers for back fat thickness trait in Yorkshire.

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