Candidate gene markers associated with production, carcass and meat quality traits in Italian Large White pigs identified using a selective genotyping approach

Italian heavy pig selection programs are based on production (average daily gain, ADG; feed gain ratio, FGR), carcass (weight of lean cuts, LC; ham weight, HW; backfat thickness, BFT) and meat quality traits of the green hams (ham weight loss at first salting, HWLFS; and visible intermuscular fat, VIF). In this study, we evaluated whether a selective genotyping approach previously designed for BFT could identify markers associated with other traits (ADG, FGR, HW, HWLFS, LC and VIF), most of which correlated with BFT. Italian Large White gilts were chosen according to their extreme estimated breeding values for BFT (275 with the most negative and 278 with the most positive EBVs) within a population of about 12,000 sib-tested pigs. A total of 736 single nucleotide polymorphisms (SNPs) in candidate genes for fat deposition and/or related traits were genotyped. After filtering, a total of 279 SNPs in 234 genes remained for association analyses that were carried out using random residuals (RRs) for the six mentioned traits. Four SNPs in three candidate genes were associated with some of the considered traits. A SNP in the exosome component 1 (EXOSC1) gene and a SNP in the glycogen phosphorylase L (PYGL) gene were associated with HWLFS RRs. Two SNPs within the TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1 (TBC1D1) gene were associated with LC RRs and suggestively associated with other performance, carcass and meat traits. Association analysis using six TBC1D1 haplotypes, inferred from four genotyped SNPs within this gene, confirmed the results of the single-marker association study. This study contributes to dissect the biological mechanisms underlying the genetic correlations among BFT, HWLFS and LC, which are critical for the sustainable implementation of tailored selection programs in heavy pigs.