Assessing Population Structure and Signatures of Selection in Wanbei Pigs Using Whole Genome Resequencing Data

SIMPLE SUMMARY: The aim of this study was to perform whole-genome resequencing on Wanbei pigs and combine its data with Asian wild boar sequencing data to assess their population structure and selection signatures. A total of 176 genes were identified as selected genes that are associated with lipid metabolism, backfat thickness, muscle, and reproduction. Genomic information may play a vital role in improving conservation strategies. ABSTRACT: Wanbei pig (WBP) is one of the indigenous pig resources in China and has many germplasm characteristics. However, research on its genome is lacking. To assess the genomic variation, population structure, and selection signatures, we resequenced 18 WBP for the first time and performed a comprehensive analysis with resequenced data of 10 Asian wild boars. In total, 590.03 Gb of data and approximately 41 million variants were obtained. Polymorphism level (θπ) ratio and genetic differentiation (fixation index)-based cross approaches were applied, and 539 regions, which harbored 176 genes, were selected. Functional analysis of the selected genes revealed that they were associated with lipid metabolism (SCP2, APOA1, APOA4, APOC3, CD36, BCL6, ADCY8), backfat thickness (PLAG1, CACNA2D1), muscle (MYOG), and reproduction (CABS1). Overall, our results provide a valuable resource for characterizing the uniqueness of WBP and a basis for future breeding.