Genome-wide detection of selective signatures in a Duroc pig population  

作　　者：DIAO Shu-qi LUO Yuan-yu MA Yun-long DENG Xi HE Ying-ting GAO Ning ZHANG Hao LI Jia-qi CHEN Zan-mou ZHANG Zhe 

机构地区：[1]Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R.China [2]Liupanshui Academy of Agricultural Sciences, Liupanshui 553001, P.R. China [3]Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education/College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China

出　　处：《Journal of Integrative Agriculture》2018年第11期2528-2535,共8页农业科学学报（英文版）

基　　金：supported by the earmarked fund for the China Agriculture Research System (CARS-35);the National Natural Science Foundation of China (31772556);the Basic Work of Science and Technology Project, China (2014FY120800);the Pearl River S&T Nova Program of Guangzhou, China (201506010027);the Guangdong S&T Project, China (2017A020208043)

摘　　要：The Duroc pig has high adaptability and feeding efficiency, making it one of the most popular pig breeds worldwide. Over long periods of natural and artificial selection, genetic footprints, i.e., selective signatures, were left in the genome. In this study, a Duroc pig population （n=715） was genotyped with the Porcine SNP60K Bead Chip and the GeneSeek Genomic Profiler （GGP） Porcine Chip. The relative extended haplotype homozygosity （REHH） method was used for selective signature detection in a subset of the population （n=368）, selected to represent a balanced family structure. In total, 154 significant core regions were detected as selective signatures （,P〈0.01）, some of which overlap with previously reported quantitative trait loci associated with several economically important traits, including average daily gain and backfat thickness. Genome annotation for these significant core regions revealed a variety of interesting candidate genes including GATA3, TAF3, ATP5C1, and FGFI. These genes were functionally related to anterior/posterior pattern specification, phosphatidylinositol 3-kinase signaling, embryonic skeletal system morphogenesis, and oxidation-reduction processes. This research provides knowledge for the study of selection mechanisms and breeding practices in Duroc and other pigs.The Duroc pig has high adaptability and feeding efficiency, making it one of the most popular pig breeds worldwide. Over long periods of natural and artificial selection, genetic footprints, i.e., selective signatures, were left in the genome. In this study, a Duroc pig population （n=715） was genotyped with the Porcine SNP60K Bead Chip and the GeneSeek Genomic Profiler （GGP） Porcine Chip. The relative extended haplotype homozygosity （REHH） method was used for selective signature detection in a subset of the population （n=368）, selected to represent a balanced family structure. In total, 154 significant core regions were detected as selective signatures （,P〈0.01）, some of which overlap with previously reported quantitative trait loci associated with several economically important traits, including average daily gain and backfat thickness. Genome annotation for these significant core regions revealed a variety of interesting candidate genes including GATA3, TAF3, ATP5C1, and FGFI. These genes were functionally related to anterior/posterior pattern specification, phosphatidylinositol 3-kinase signaling, embryonic skeletal system morphogenesis, and oxidation-reduction processes. This research provides knowledge for the study of selection mechanisms and breeding practices in Duroc and other pigs.

关 键 词：DUROC selective signature candidate genes REHH 

分 类 号：S828[农业科学—畜牧学]