The effects of selection on the genomic architecture of the Italian Large White and Duroc heavy pigs

Artificial selection may cause an increasing of homozygosity in circumscribed regions of the genome and lead to allele drift. This is particularly important for selection nuclei of pure breeds. In this work we analysed the genome of the Italian Large White (ILW) and Italian Duroc (ID) breeds, that are purposely selected for the heavy pig breeding industry, to identify regions of high homozygosity. A total of 1,953 Italian Large White and 460 Italian Duroc pigs were genotyped with the Illumina PorcineSNP60 BeadChip. Filtering was performed to remove poor quality single nucleotide polymorphisms (SNPs) having call rate<0.9 that were then imputed whereas no other filter was applied. The Runs of Homozygosity (ROH) analyses were performed with the sliding window-based option of the Plink 1.9 software, allowing a minimum of 30 SNP to define a ROH. Then, for each SNP, the percentage of the number of animals that have a ROH containing the SNP was calculated and the top 0.994 percentile of the SNPs empirical distribution was considered. The analyses of the ILW detected four regions, three on porcine chromosome (SSC) 1 and one region on SSC14, with size from ~1 to 5 Mb and with maximum peak of shared regions of 70% on SSC1. The analysis of the ID pigs showed several SNPs shared by more than the 50% of the animals, particularly two regions on SSC9 and SSC15, with maximum peak of 95% on SSC15. The detected regions contained genes involved in functions such as DNA repair and biosynthesis of cellular amino acid. The possible effects of these regions and the genes included in relation to production traits still need to be analysed. Partially funded by European Union’s H2020 RIA program (grant agreement no. 634476).