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

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. SUPPLEMENTARY INFORMATION: Supplementary information accompanies this paper at 10.1186/s40104-020-00520-8.