Monitoring allele frequency trends associated with resistance to relevant diseases in Italian heavy pig breeds over the last three decades

Infectious diseases have a significant economic impact on the global pig breeding industry. Recently, a few genetic markers associated with disease resistance have been identified and utilized in marker-assisted selection (MAS) in a few pig populations, as part of disease control programs. Neonatal Diarrhea (ND) caused by enterotoxigenic Escherichia coli, and Porcine Reproductive and Respiratory Syndrome (PRRS), caused by PRRS virus (PRRSV), are diseases of high priority for the pig industry. The Italian heavy pig industry is primarily based on three major breeds: Italian Large White, Italian Landrace and Italian Duroc. Selection programs for these breeds begun in the 1990s with a focus on improving meat quality and carcass traits necessary for producing high quality Protected Designation of Origin dry-cured hams. These programs have since been refined to include enhancing resistance against relevant diseases, measured indirectly with a new estimated breeding value that incorporates this information. Additionally, specific efforts have been made to increase resistance against ND by using associated single nucleotide polymorphisms (SNPs). In this study, we monitored allele frequency trends over the last three decades in the three Italian heavy pig breed populations using linked markers to the mucin 4 (MUC4) gene, associated with resistance to ND, and SNP rs80800372 (also known as WUR10000125) associated with resistance to PRRS. We genotyped over 20,000 pigs born during this time window with a high-density SNP panel and extracted the relevant markers and haplotypes. No significant allele frequency change for the WUR10000125 marker occurred in all breeds over this period, which may reflect the indirect selection on this disease and the low frequency of the positive allele in all breeds. For the MUC4 linked markers, the Italian Duroc breed reached fixation for the positive allele, which increased in the other two breeds. We are continuing to monitor the genetic background of the Italian heavy pig breed population with the final goal of enhancing the sustainability of the selection and breeding programs. Research supported by PSRN (Programma di Sviluppo Rurale Nazionale) SUIS and SUIS-2 projects (co-funded by the European Agricultural Fund for Rural Development of the European Union and by the Italian Ministry of Agriculture, Food and Forestry—MASAF).