Mining high density SNP chipdata and whole genome sequencing information to identify putative unfavorable alleles in pig breeds

Deleterious and usually recessive alleles are present at very low frequency and in heterozygous state in all livestock populations. Their frequency could increase if these alleles are in linkage disequilibrium with favorable QTL alleles or if heterozygous animals show heterosis for some production traits under selection.The homozygous state of these alleles is usually not compatible with life and therefore it is not possible to observed homozygous adult animals. Consequently, carrier animals might have reduced reproduction performances, depending on the frequency of these alleles in the breeding population. In this study, we mined high density single nucleotide polymorphism (SNP) chip data from three Italian pig breeds (Italian Large White, n = 5528, ItalianLandrace, n = 3470; Italian Duroc, n = 1354) to identify genome regions carrying putative unfavorable and deleterious alleles. The strategy was based on SNP allele frequencies and the expected occurrence of homozygous genotypes following population genetic rules over the absence of these genotypes in the three pig breeds, after filtering SNP data with stringent criteria for genotyping errors and other genotyping biases. Then, we compared SNP chip data with whole genome sequencing information obtained from 160 pigs of the three targeted breeds to identify loss of function variants in the candidate genome regions. Overall, we detected five genome regions carrying putative unfavourable alleles. Their estimated allele frequency ranged from 0.07 to 0.17, suggesting that some of them might be linked to favourable alleles affecting production traits under selection. The identification of loss of function variants in key genes located in these regions suggests some biological mechanisms that would explain their deleterious effect. These results provide genomic markers that can be used to design targeted breeding and selection programs aimed to reduce the frequency of unfavourable alleles in the Italian pig populations and reduce their negative impact on reproduction performances by avoiding carrier-carrier mating.