The genomic inbreeding landscape of Italian heavy pig breeds over the last decades

The level of inbreeding in a population should be limited to avoid the inbreeding depression and maintain variability needed to assure long term genetic progress. Inbreeding coefficient (FPED) is usually calculated using pedigree information. Single nucleotide polymorphism (SNP) genotyping tools give the possibility to calculate genomic inbreeding parameters. The proportion of the autosomal genome covered by runs of homozygosity (ROH) can be used to estimate the level of genomic inbreeding (FROH). The breeding program of Italian pig breeds started about 25 years ago. In this work, we retrospectively analysed FROH over this period in Italian Large White (ILW) and Italian Duroc (ID) heavy pig breeds and compared this parameter with FPED. A total of 1,420 ILW and 572 ID pigs born over the last 25 years have been genotyped with the Illumina PorcineSNP60 BeadChip. ROH were identified with PLINK version 1.9, considering a minimum of 15 SNPs, and a minimum length of 1 Mbp. Then FROH was computed for all animals and averaged over all animals born by year. Averaged FROH over all considered years was higher in ID than in ILW and was constant over all analysed time window. FROH and FPED were parallel for both breeds over the same period. The results indicated that both FROH and FPED can be used to manage inbreeding levels in Italian heavy pig breeds.