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논문 기본 정보

자료유형
학술저널
저자정보
Kim, HyoYoung (Department of Agricultural Biotechnology, Seoul National University) Caetano-Anolles, Kelsey (Department of Animal Sciences, University of Illinois) Seo, Minseok (Interdisciplinary Program in Bioinformatics, Seoul National University) Kwon, Young-jun (Interdisciplinary Program in Bioinformatics, Seoul National University) Cho, Seoae (C&K Genomics Inc., Seoul National University Research Park) Seo, Kangseok (Department of Animal Science and Technology, College of Life Science and Natural Resources, Sunchon National University) Kim, Heebal (Department of Agricultural Biotechnology, Seoul National University)
저널정보
한국유전체학회 Genomics & informatics Genomics & informatics 제13권 제4호
발행연도
2015.1
수록면
137 - 145 (9page)

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Selective sweep can cause genetic differentiation across populations, which allows for the identification of possible causative regions/genes underlying important traits. The pig has experienced a long history of allele frequency changes through artificial selection in the domestication process. We obtained an average of 329,482,871 sequence reads for 24 pigs from three pig breeds: Yorkshire (n = 5), Landrace (n = 13), and Duroc (n = 6). An average read depth of 11.7 was obtained using whole-genome resequencing on an Illumina HiSeq2000 platform. In this study, cross-population extended haplotype homozygosity and cross-population composite likelihood ratio tests were implemented to detect genes experiencing positive selection for the genome-wide resequencing data generated from three commercial pig breeds. In our results, 26, 7, and 14 genes from Yorkshire, Landrace, and Duroc, respectively were detected by two kinds of statistical tests. Significant evidence for positive selection was identified on genes ST6GALNAC2 and EPHX1 in Yorkshire, PARK2 in Landrace, and BMP6, SLA-DQA1, and PRKG1 in Duroc. These genes are reportedly relevant to lactation, reproduction, meat quality, and growth traits. To understand how these single nucleotide polymorphisms (SNPs) related positive selection affect protein function, we analyzed the effect of non-synonymous SNPs. Three SNPs (rs324509622, rs80931851, and rs80937718) in the SLA-DQA1 gene were significant in the enrichment tests, indicating strong evidence for positive selection in Duroc. Our analyses identified genes under positive selection for lactation, reproduction, and meat-quality and growth traits in Yorkshire, Landrace, and Duroc, respectively.

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