Identification of breed-specific SNPs for genetic assessment of differentiation of commercial pig breeds

Identification of specific genetic markers that determine interbreed differences and “selection signatures” in commercial pig breeds will allow for the development of more effective strategies for targeted breeding and improvement of animal genetic potential. The aim of this study is to analyze the whole-genome data of five commercial pig breeds using the FST method to identify markers that characterize interbreed differentiation, as well as to assess the intra-breed stratification caused by selective breeding. Special attention is given to identifying potential “selection signatures” that are specific to each breed. This study assessed the genetic differentiation among commercial pig breeds (duroc, berkshire, pietrain, hampshire, landrace) using the fixation index (FST), calculated based on genome-wide genotyping data for single nucleotide polymorphisms (SNPs). A moderate level of interbreed divergence was observed, with the highest pairwise FST values recorded for duroc – berkshire (0.19), duroc – pietrain (0.18), and duroc – landrace (0.17), while the lowest differentiation was noted between pietrain and landrace (0.14). Genome-wide FST distribution analysis enabled the identification of highly differentiated SNPs (above the 99th percentile), with their number ranging from 126 to 167 across comparisons. The greatest concentration of these SNPs was observed on chromosomes SSC1, SSC13, SSC4, and SSC6, indicating the presence of selective «hotspots» likely involved in the regulation of productivity – and adaptation-related traits. Several SNPs were consistently detected across multiple breed comparisons, highlighting their breed specificity and potential functional relevance. Functional annotation has revealed that these SNPs are located within genes, including PCDHB7 and PPP2R2B, which are characterized by tissue-specific expression in muscle and adipose tissues, and are implicated in the regulation of metabolic processes. Of particular interest is a SNP ASGA0079413 located within the TFEC gene, identified in Landrace pigs. Given its membership and its known role in pigment cell differentiation, this gene may contribute to the formation of white coat color, as well as to immune and metabolic functions.