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

Journal of Animal Science and Biotechnology

Yuhua Fu¹  Shuhong Zhao¹  Jingya Xu¹  Dong Yin¹  Mengjin Zhu¹  Xiaolei Liu¹  Yang Zhou¹  Lilin Yin¹  Xinyun Li¹  Yan Hu¹  Zhenshuang Tang¹  Mei Yu¹ 

[1] 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;

关键词: Breed feature;    CNV;    GWAS;    InDel;    Pig;    SNP;   

DOI  :  10.1186/s40104-020-00520-8

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown