The SNPs discovery in RRLs from DNA pools of Nero Siciliano pigs with extreme and divergent phenotypes for the Back Fat Thickness (BFT) tract

SNPs discovery from DNA pools of nero Siciliano pig extreme and divergent phenotypes

Abstract

Fat deposition is a key biological process that has implications in pig economic management. This process affects carcass quality and aptitude for the typical product productions such as salami, sausages and of cured ham. This study aimed to detect single nucleotide polymorphisms (SNPs) that could be associated with the backfat thickness (BFT) tract in Nero Siciliano pigs. The Food and Agriculture Organization (FAO) has expressed concern about the lack of interest in local breeds compared to high-output animals and conservation programs have been implemented by various countries worldwide. Genomic DNA from two groups of Nero Siciliano pigs with divergent phenotypes for BFT was pooled and digested with BsuRI (HaeIII) restriction enzyme for preparation of reduced representation libraries (RRLs). The two RRLs produced 4124595 (BFT+) and 4052107 (BFT-) sequenced reads, were mapped on Sus scrofa reference genome (Sscrofa 11.1 assembly). SNP calling was performed using SNAPE, a software that implements a Bayesian approach for SNP calling in pooled samples. 47,791 putative SNPs were called by SNAPE, of these 32,235 (67.4%) were polymorphic while 15,556 (32.5%) were monomorphic. Of all SNPs detected in this study, 22 showed enriched alleles in one or the other RRLs. These SNPs, some of these localised in genes involved in fat metabolism, might be potential markers associated with BFT in Nero Siciliano pig. In this study, we identified SNPs potentially associated with BFT that might be utilized for applications in breeding programs. Attitude to high-fat deposition (in particular in neck, withers and back) for the Nero Siciliano pig is known and our results could contribute to explain the biology of fat metabolism in this breed.