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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).

Next generation sequencing applied in pigs have recently produced re-sequenced pig genome data from different individuals belonging to a large variety of breeds. The availability of these large datasets is opening new opportunities to mine public nucleotide archives and identify mutations that could putatively affect economic relevant traits. Moreover, resequencing data from pooled pig DNA could provide cost-effective whole genome information from a large number of animals. In this study, we mined 110 individual pig genomes retrieved from the European Nucleotide Archive and from proprietary datasets generated from pigs of 28 different breeds. This dataset was integrated from 8 pooled whole genome resequencing datasets generated from 35 individuals each from 8 distinct commercial or autochthonous breeds (Italian Large White, Italian Duroc, Italian Landrace, Apulo Calabrese, Cinta Senese, Casertana, Mora Romagnola, Nero Siciliano), respectively. Individual and pooled pig genome datasets were searched for polymorphisms in 135 annotated candidate genes, including 25 genes involved in androsterone and skatole biochemical related pathways. Short reads from these genomes were aligned using bowtie to a customized reference sequence generated from the reference pig genome, including sequence of selected genes (with depth ranging from 4 to 40X for each genome). A total of 100k variants were identified (2.3% in coding regions with about 500 missense mutations and a few other potential functional mutations). About 15% of these numbers refers to genes encoding enzymes involved in the androsterone and skatole biochemical pathways. This study provided an overview of the variability in targeted gene regions potentially involved in determining boar taint in pigs. Partially funded by European Union's H2020 RIA program (grant agreement no. 634476). Abstract reflects the authors' view. European Union Agency is not responsible for any use that may be made of the information it contains.

Animal genetic resources are important reservoirs of genetic diversity derived by distinct selection pressures or as result of adaptation to production conditions. The TREASURE project has investigated genetic variability in 20 European autochthonous pig breeds with the aim to describe their singularity, evaluate their adaptation, develop new methodologies for their management and identify DNA markers for breed allocation and meat authentication. Genomic data have been obtained by genotyping candidate gene markers and high density single nucleotide polymorphism arrays in ~48 animals from each breed and by whole genome resequencing. Description of genetic diversity has been obtained using several parameters. Runs of homozygosity and genomic inbreeding measures have been correlated with pedigree inbreeding coefficients. A few breed specific markers have been identified and applied. Genome wide association studies have identified genomic regions affecting unique phenotypes. This project represents one of the few examples of exploitation of genomic information that not only benefits the investigated animal genetic resources but also can provide useful information that could impact commercial populations. Funded by European Union's H2020 RIA program (grant agreement no. 634476).