Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

作     者：Jingya Xu Yuhua Fu Yan Hu Lilin Yin Zhenshuang Tang Dong Yin Mengjin Zhu Mei Yu Xinyun Li Yang Zhou Shuhong Zhao Xiaolei Liu Jingya Xu;Yuhua Fu;Yan Hu;Lilin Yin;Zhenshuang Tang;Dong Yin;Mengjin Zhu;Mei Yu;Xinyun Li;Yang Zhou;Shuhong Zhao;Xiaolei Liu

作者机构：Key Laboratory of Agricultural Animal GeneticsBreeding and ReproductionMinistry of Education&Key Laboratory of Swine Genetics and BreedingMinistry of Agriculture&College of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan 430070HubeiPR China 

出 版 物：《Journal of Animal Science and Biotechnology》 (畜牧与生物技术杂志（英文版）)

年 卷 期：2021年第12卷第2期

页      面：492-507页

核心收录：

学科分类：0905[农学-畜牧学] 09[农学] 090501[农学-动物遗传育种与繁殖] 

基　　金：supported by the Key Project of National Natural Science Foundation of China(31790414) the National Natural Science Foundation of China(31702087,31902156,31730089) Fundamental Research Funds for the Central Universities(2662020DKPY007,2662017QD016) the National Swine Industry Technology System(CARS-35) 

主　　题：Breed feature CNV GWAS InDel Pig SNP 

摘      要：Background:A large number of pig breeds are distributed around the world,their features and characteristics vary among breeds,and they are valuable *** the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig ***:In this study,we performed GWAS using a standard mixed linear model with three types of genome variants(SNP,InDel,and CNV)that were identified from public,whole-genome,sequencing data *** used 469 pigs of 57 breeds,and we identified and analyzed approximately 19 million SNPs,1.8 million InDels,and 18,016 *** defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes,which included coat color,ear shape,gradient zone,body weight,body length,and body height.A total of 37 candidate genes was identified,which included 27 that were reported previously(e.g.,PLAG1 for body weight),but the other 10 were newly detected candidate genes(e.g.,ADAMTS9 for coat color).Conclusion:Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits.