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

Wei Zhang; Min Yang; Mei Zhou; Yuanlang Wang; Xudong Wu; Xiaodong Zhang; Yueyun Ding; Guiying Zhao; Zongjun Yin; Chonglong Wang

doi:10.3389/fgene.2020.566255

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

Front Genet. 2020 Sep 17:11:566255. doi: 10.3389/fgene.2020.566255. eCollection 2020.

Authors

Affiliations

¹ Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, China.
² College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.
³ Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China.

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 (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.

Keywords: Anqing six-end-white pig; FST; SNP; signatures of selection; θπ.