Selective Sweeps in the Austrian Turopolje and Other Commercial Pig Populations

Simple Summary In our study, our primary aim was to identify signatures of selection in Turopolje pigs, a local breed, and four commercial pig breeds (Large White, Landrace, Pietrain, and Duroc). We conducted an extensive analysis of genetic data from 485 pigs, examining 54,075 specific genetic markers. Our focus was on genes that have undergone positive selection pressures. Consistent with previous research, we identified two key genes, PTBP2 and DPYD, as consistently influenced by selection in all the pig breeds we studied. These genes play essential roles in muscular development, a critical factor for pigs and other species. Additionally, in the Large White breed, we discovered several genes associated with traits such as body weight, production efficiency, meat quality, and more. In the Duroc breed, we detected different genes linked to similar traits. Our findings provide valuable insights into the genetic changes driven by selective pressures in local and commercial pig breeds. This knowledge can enhance our understanding of pig breeding mechanisms and contribute to more efficient and sustainable pig farming practices. Our study underscores the significance of employing various genomic methodologies to identify genetic signatures of selection, fulfilling the primary aim of our research, and offers important insights into pig breed diversity. Abstract The goal of our study was to identify signatures of selection in the Turopolje pigs and other commercial pig breeds. We conducted a comprehensive analysis of five datasets, including one local pig breed (Turopolje) and four commercial pig breeds (Large White, Landrace, Pietrain, and Duroc), using strict quality control measures. Our final dataset consisted of 485 individuals and 54,075 single nucleotide polymorphisms (SNPs). To detect selection signatures within these pig breeds, we utilized the XP-EHH and XP-nSL methodologies, which allowed us to identify candidate genes that have been subject to positive selection. Our analysis consistently highlighted the PTBP2 and DPYD genes as commonly targeted by selection in the Turopolje breed. DPYD is associated with muscular development in pigs and other species and PTBP2 emerges as one of the potential genes linked to seminal characteristics. Furthermore, in the Large White breed, a number of genes were detected with the two methods, such as ATP1A1, CASQ2, CD2, IGSF3, MAB21L3, NHLH2, SLC22A15, VANGL1. In the Duroc breed, a different set of genes was detected, such as ARSB, BHMT, BHMT2, DMGDH, JMY. The function of these genes was related to body weight, production efficiency and meat quality, average daily gain, and other similar traits. Overall, our results have identified a number of genomic regions that are under selective pressure between local and commercial pig breeds. This information can help to improve our understanding of the mechanisms underlying pig breeding, and ultimately contribute to the development of more efficient and sustainable pig production practices. Our study highlights the power of using multiple genomic methodologies to detect genetic signatures of selection, and provides important insights into the genetic diversity of pig breeds.