Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig

Identification of genomic signatures of selection that help reveal genetic mechanisms underlying traits in domesticated pigs is of importance. Anqing six-end-white pig (ASP), a representative of the native breeds in China, has many distinguishing phenotypic characteristics. To identify the genomic signatures of selection of the ASP, whole-genome sequencing of 20 ASPs produced 469.01 Gb of sequence data and more than 26 million single-nucleotide polymorphisms. Combining these data with the available whole genomes of 13 Chinese wild boars, 157 selected regions harboring 48 protein-coding genes were identified by applying the polymorphism levels (θπ) and genetic differentiation ( F ST ) based cross approaches. The genes found to be positively selected in ASP are involved in crucial biological processes such as coat color ( MC1R ), salivary secretion ( STATH ), reproduction ( SPIRE2 , OSBP2 , LIMK2 , FANCA , and CABS1 ), olfactory transduction ( OR5K4 ), and growth ( NPY1R , NPY5R , and SELENOM ). Our research increased the knowledge of ASP phenotype-related genes and help to improve our understanding of the underlying biological mechanisms and provide valuable genetic resources that enable effective use of pigs in agricultural production.