Identifying Selection Signatures for Backfat Thickness in Yorkshire Pigs Highlights New Regions Affecting Fat Metabolism

• Main Authors: Haoran Ma, Saixian Zhang, Kaili Zhang, Huiwen Zhan, Xia Peng, Shengsong Xie, Xinyun Li, Shuhong Zhao, Yunlong Ma
• Format: Article
• Language: English
• Published: MDPI AG 2019-03-01
• Series: Genes
• Subjects: trait-specific selection signatures; population differentiation-based methods; functional annotation
• Online Access: https://www.mdpi.com/2073-4425/10/4/254

Identifying the genetic basis of improvement in pigs contributes to our understanding of the role of artificial selection in shaping the genome. Here we employed the Cross Population Extended Haplotype Homozogysity (XPEHH) and the Wright&#8217;s fixation index (F_ST) methods to detect trait-specific selection signatures by making phenotypic gradient differential population pairs, and then attempted to map functional genes of six backfat thickness traits in Yorkshire pigs. The results indicate that a total of 283 and 466 single nucleotide polymorphisms (SNPs) were identified as trait-specific selection signatures using F_ST and XPEHH, respectively. Functional annotation suggested that the genes overlapping with the trait-specific selection signatures such as <i>OSBPL8</i>, <i>ASAH2</i>, <i>SMCO2</i>, <i>GBE1,</i> and <i>ABL1</i> are responsible for the phenotypes including fat metabolism, lean body mass and fat deposition, and transport in mouse. Overall, the study developed the methods of gene mapping on the basis of identification of selection signatures. The candidate genes putatively associated with backfat thickness traits can provide important references and fundamental information for future pig-breeding programs.