Dissecting the genetic variability of major genes for pig production traits using whole genomesequencing data.

Whole genome sequencing (WGS) datasets produced from next generation sequencing technologies are making it possible to obtain a comprehensive evaluation of the level of genetic variability within and across breeds and populations in many livestock species and to infer their genetic history and relevant population genetic information useful to manage these animal genetic resources. In this study, we mined WGS datasets from about 500 individual pigs or groups of pigs (obtained from DNApools) belonging to 30 European and 14 Asian breeds, European and Asian wild boars and other species of the Sus genus (Sus barbatus, S. cebifrons, S. celebensis and S. verrucosus) closely related to Sus scrofa. Two thirds of the datasets were retrieved from the European Nucleotide Archive (ENA) or from previous projects and one-third was newly produced for this study and derived from Italian Large White, Italian Landrace and Italian Duroc pigs. Datasets retrieved from ENA were pre-filtered according to a minimum averaged depth of sequencing of 10× whereas the average depth of sequencing of the newly produced WGS datasets was about 23×. A total of 150 genes were selected according to their already established role in affecting relevant production traits (e.g. growth rate, lean meat and fat deposition, reproduction performances, taste preference, meat quality, including boar taint). Short reads from these genomes were first aligned using bowtie to a customized reference sequence generated from the reference pig genome, including sequence of the selected genes. Variant calling was performed with samtools software. The Ensembl Variant Effect Predictor tool was used to inspect the consequences of the identified variants and potentially deleterious mutations were detected with SIFT. About 2.3% of the detected variants were in coding regions and included a total of 340 missense mutations and other variants with predicted functional effects (e.g. stop codon gains/losses, frameshift mutations). Substantial differences in allele frequencies and allele distributions were observed for these putative relevant variants between European and Asian pig breeds and across the other Sus species. This study provided a landscape genome picture of variants that might explain part of the genetic variability of important production traits in pigs. Acknowledgements This study was supported by PRIN2017 MUR funds (PigPhenomics project)