The genomic inbreeding trends in Italian heavy pig breeds over the last 25 years.

The control of inbreeding is fundamental in managing livestock species. A high level of inbreeding leads to a decline in performance and fitness, a phenomenon known as inbreeding depression, and to the emergence of deleterious or lethal alleles that, in absence of inbreeding, would remain at a low frequency in the population. The Italian pig industry, mainly oriented to the production of the Protected Designation of Origin (PDO) dry-cured ham, is based on 3 heavy pig breeds, namely Italian Large White (ILW), Italian Landrace (IL) and Italian Duroc (ID). The breeding program of these breeds started about 25 years ago and information about pedigree has been recorded in the last decades. Inbreeding coefficient (FPED) is traditionally calculated using pedigree records. With the advent of high-throughput genotyping platforms, new methods to calculate the genomic inbreeding have been developed, directly using genome information. One of the most effective methods is the detection of long stretches of the genome that is homozygous at each adjacent locus, called runs of homozygosity (ROH). The proportion of the autosomal genome covered by ROH can be used to estimate the level of genomic inbreeding (FROH) and the history of the population. In this work, we retrospectively analyzed FPED and FROH over this period in these 3 breeds. A total of 3,400 ILW, 1940 ILA and 1,100 ID pigs born over the last 25 years have been genotyped with the 70K Illumina GGP Porcine HD and Illumina Porcine60K SNPchips. FPED was computed with Inbupgf90 software from pedigree data. ROH were identified with PLINK version 1.9. Then FROH and FPED were averaged over all animals born by year. Averaged FROH over all considered years was higher in ID; the trend of FPED and FROH was increasing during years for all breeds. It is worth to notice that FPED trend had a strongest slope with respect to FROH, indicating that, at a biological level, decades of selection did not worsen the inbreeding level of the breeds. The results indicated that both FROH and FPED can be used to manage inbreeding levels in Italian heavy pig breeds and provided information that could be useful to manage these pig genetic resources.