Mining whole genome resequencing data to identify functional mutations in boar taintcandidate genes

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.