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

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

JOURNAL=Frontiers in Genetics

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.566255

DOI=10.3389/fgene.2020.566255

ISSN=1664-8021

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