Large scale genome-wide association studies for seven production traits in Italian heavy pigs

The Italian heavy pig selection program is mainly designed to obtain suitable raw materials (i.e. green legs) for the production of Protected Designation of Origin (PDO) dry-cured hams, which overall represent an economic value of more than 3 billion € per year. Several traits are collected on pigs that are evaluated in the sib testing scheme: (1) indicators of the overall fat/lean content of the animals, including backfat thickness, ham weight and lean cuts; (2) traits related to performance and efficiency, including average daily gain and feed/gain ratio; (3) peculiar traits for dry-cured ham production, including visible intermuscular fat and ham weight loss at first salting. In this study, we carried out genome-wide association studies for these traits in the three traditional Italian breeds included in the heavy pig selection program: Italian Large White, Italian Landrace and Italian Duroc breeds. A total of more than 10,000 pigs have been genotyped with two single nucleotide polymorphism (SNP) arrays: Illumina PorcineSNP60 BeadChip and GeneSeek/Neogen GGP Porcine HD arrays. Genome scans (single-SNP and haplotype-based) were performed with GEMMA v.0.98. Several QTL regions affecting these traits were obtained. Results were poorly overlapping between traits and breeds, confirming what was obtained in our previous studies based on a smaller sample size. Overall, this study further characterized the genetic architecture of these production traits and provided additional information for improving those genomic selection plans currently running in these breeds.