How directional artificial selection has shaped the genome of Italian heavy pig breeds.

The breeding programs of the Italian heavy pig breeds (Italian Duroc, Italian Landrace and Italian Large White) started in 1990, having as main objectives the needs of the Italian dry-cured ham protected designation of origin (PDO) value chains. This directional selection was based on several traits that substantially improved performance, reproduction and carcass traits of the three breeds while maintaining the meat quality for seasoning. Because of the selection, the genetic background of the three breeds diverged from the cosmopolitan Duroc, Landrace and Large White breeds used in other production systems. In this study, we monitored how this selection acted at the genomic level on the Italian heavy pig breeds. About 13,000 pigs of the three Italian breeds, born over almost four decades, were genotyped with a high-density SNP array. Over time changes of single marker and haplotype frequencies were evaluated, using a logistic regression model. A total of about 350-500 haplotypes in the three breeds significantly changed their frequency providing a picture of the genomic regions that were indirectly modified by the directional artificial selection programs operating over this period. Acknowledgements: Funded by the Programma di Sviluppo Rurale Nazionale (PSRN) SUIS-2, co-funded by the European Agricultural Fund for Rural Development of the European Union and by the MASAF.