Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed
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(2020) 11:115
RESEARCH
Open Access
Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features Jingya Xu†, Yuhua Fu†, Yan Hu, Lilin Yin, Zhenshuang Tang, Dong Yin, Mengjin Zhu, Mei Yu, Xinyun Li, Yang Zhou*, Shuhong Zhao* and Xiaolei Liu*
Abstract Background: A large number of pig breeds are distributed around the world, their features and characteristics vary among breeds, and they are valuable resources. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds. Results: 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 sets. We used 469 pigs of 57 breeds, and we identified and analyzed approximately 19 million SNPs, 1.8 million InDels, and 18,016 CNVs. We 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. Keywords: Breed feature, CNV, GWAS, InDel, Pig, SNP
Background With more than one billion individuals alive at any time, the domestic pig (Sus scrofa domestica) is one of the most important livestock animals in the world. Domestication was accomplished well before 9,000 years ago [1, 2], and a wide range of breeds were developed to meet various demands of human beings. Both domestication * Correspondence: [email protected]; [email protected]; [email protected] † Jingya Xu and Yuhua Fu contributed equally to this work. Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
and artificial selection led to rapid phenotypic changes and resulted in distinct features and characteristics among breeds. With different domestication and breeding goals, a large number of pig breeds became distributed throughout the world, and some of their characteristic features varied from one breed to another. These characteristics fall broadly into two categories, one is production features, which include growth, reproduction, carcass and meat quality, and the other consists of biological characteristics, which include body shape, appearance, and coat color. The Pietrain pig breed, which is native to Belgium, was bred as a lean pig breed and has the outstanding
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