Signatures of selection in Italian heavy pigs: how genetic programs for PDO ham productions are shaping the genomes of cosmopolitan breeds

Breeding and selection programs designed for Italian heavy pigs have enhanced specific meat quality and carcass traits, in addition to several other traits, in line with the needs of the Protected Designation of Origin (PDO) dry-cured ham production systems. These programs have specific breeding goals for each of the breeds (Italian Large White, Italian Landrace and Italian Duroc) that compose the terminal pigs used for ham production. Selection programs may have produced signatures of selection left in the genome of the improved breeds, where relevant QTL or genes are located. In this work, we have dissected the genomic architecture of these three breeds by combining signature selection analyses and genome-wide association studies of the most relevant production traits. A total of 9089 pigs (4626 Italian Large White; 3253 Italian Landrace; and 1210 Italian Duroc) have been genotyped with high-density single nucleotide polymorphism (SNP) chip. Several population genomic parameters and features were defined or calculated in these breeds and, where, relevant, in the pairwise comparisons: runs of homozygosity (ROH) islands, Integrated Haplotype score (iHS) and extended haplotype homozygosity (XP-EHH). Genome-wide association studies have been also performed for several production traits. Breed-specific ROH islands (i.e. shared by at least 50% of the animals) were detected on three, three and seven different chromosomes in the Italian Large White, Italian Landrace and Italian Duroc breeds, respectively. Several ROH signals were confirmed with the iHS patterns. Common overlapping signals between breeds were identified, including genes for coat colour such as OCA2. Some signatures of selection regions, therefore in genomic regions of low variability, fell within QTLs. Some of the overlapping QTL were Visible intermuscular fat in Large White and Ham weight at first salting in Duroc. The obtained results provide a landscape genomic picture obtained by years of breeding and selection in Italian heavy pig breeds.