Signatures of selection analyses reveal genomic differences among three heavy pig breeds that constitute the genetic backbone of a dry-cured ham production system

The Italian pig farming industry is unique in its focus on raising heavy pigs primarily for the production of high-quality dry-cured hams. These products require pigs to be slaughtered at a live weight of around 170 kg at 9 months of age. The primary breeds used in this system are Italian Duroc, Italian Landrace, and Italian Large White which are crossed to produce lines that meet standard requirements. Over the past four decades, selection and breeding programmes for these breeds have been subjected to distinct selective pressures to highlight the characteristics of each breed. In this study, we investigated the genome of these breeds by analysing high-density single nucleotide polymorphism data from over 9 000 pigs to scan for signatures of selection using four different methods, two within breeds and two across breeds. This allowed to identify the genomic regions that differentiate these breeds as well as any relevant genes and biological terms. On a global scale, we found that the Italian Duroc breed exhibited a higher genetic differentiation from the Italian Landrace and Italian Large White breeds, with a pairwise FST value of 0.20 compared with the 0.13 between Italian Landrace and Italian Large White. This may reflect either their different origins or the different breeding goals, which are more similar for the Italian Landrace and Italian Large White breeds. Despite these genetic differences at a global level, few signatures of selection regions reached complete fixation, possibly due to challenges in detecting selection linked to quantitative polygenic traits. The differences among the three breeds are confirmed by the low level of overlap in the regions detected. Genetic enrichment analyses of the three breeds revealed pathways and genes related to various productive traits associated with growth and fat deposition. This may indicate a common selection direction aimed at enhancing specific production traits, though different biological mechanisms are likely targeted by the same directional selection in these three breeds. Therefore, these genes may play a critical role in determining the distinctive characteristics of Italian Duroc, Italian Landrace, and Italian Large White, and potentially influence the traits in crossbred pigs derived from them. Overall, the insights gained from this study will contribute to understanding how directional selection has shaped the genome of these heavy pig breeds and to better address selection strategies aimed at enhancing the meat processing industry linked with dry-cured ham production chains.