A comparative genome analysis across pig breeds can help to identify putative deleterious alleles

The small effective population size of many highly selected livestock breeds or nuclei can lead to an increased frequency of unfavourable and usually deleterious alleles, in particular if they are in linkage disequilibrium with other favourable QTL alleles. Animals that are homozygous for these negative alleles are, however, not observed in the adult population as the genotype is not usually compatible with a productive life. In this study, we used high density single nucleotide polymorphisms (SNPs) analysed in more than 10,000 heavy pigs belonging to three breeds (Italian Large White, Italian Landrace and Italian Duroc) and whole genome sequencing data obtained in a subset of these animals to define a comparative-across breed strategy that can identify putative deleterious alleles segregating in one or more breeds. The across-breed strategy made it possible to filter out genotyping errors and other genotyping biases that would create statistical biases in the identification of candidate genomic regions harbouring deleterious alleles. Combining this information with whole genome sequencing data, these results provided genomic markers that can be used to design targeted breeding and selection programs aimed to reduce the frequency of deleterious alleles in the Italian pig population.