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

Abstract

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 (<i>F</i> _<i>ST</i> ) based cross approaches. The genes found to be positively selected in ASP are involved in crucial biological processes such as coat color ( <i><i>MC1R</i></i> ), salivary secretion ( <i><i>STATH</i></i> ), reproduction ( <i><i>SPIRE2</i></i> , <i><i>OSBP2</i></i> , <i><i>LIMK2</i></i> , <i><i>FANCA</i></i> , and <i><i>CABS1</i></i> ), olfactory transduction ( <i><i>OR5K4</i></i> ), and growth ( <i><i>NPY1R</i></i> , <i><i>NPY5R</i></i> , and <i><i>SELENOM</i></i> ). 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.