Exome capture with heterologous enrichment in pig (Sus scrofa)

The discovery of new protein-coding DNA variants related to carcass traits is very important for the Italian pig industry, which requires heavy pigs with higher thickness of subcutaneous fat for Protected Designation of Origin (PDO) productions. Exome capture techniques offer the opportunity to focus on the regions of DNA potentially related to the gene and protein expression. In this research a human commercial target enrichment kit was used to evaluate its performances for pig exome capture and for the identification of DNA variants suitable for comparative analysis. Two pools of 30 pigs each, crosses of Italian Duroc X Large White (DU) and Commercial hybrid X Large White (HY), were used and NGS libraries were prepared with the SureSelectXT Target Enrichment System for Illumina Paired-End Sequencing Library (Agilent). A total of 140.2 M and 162.5 M of raw reads were generated for DU and HY, respectively. Average coverage of all the exonic regions for Sus scrofa (ENSEMBL Sus_scrofa.Sscrofa10.2.73.gtf) was 89.33X for DU and 97.56X for HY; and 35% of aligned bases uniquely mapped to off-target regions. Comparison of sequencing data with the Sscrofa10.2 reference genome, after applying hard filtering criteria, revealed a total of 232,530 single nucleotide variants (SNVs) of which 20.6%mapped in exonic regions and 49.5% within intronic regions. The comparison of allele frequencies of 213 randomly selected SNVs from exome sequencing and the same SNVs analyzed with a Sequenom MassARRAY1 system confirms that this “human-on-pig” approach offers new potentiality for the identification of DNA variants in protein-coding genes. Introduction For PDO (Protected Designation of Origin) ham production, the Italian pig industry requires heavy pigs, reared for 9 months and slaughtered at 160 kg live weight and with a carcass lean percentage ranging from 40% to 55%. According to the production guidelines (EC No: IT-PDO-0117-01149) [1], pigs must belong to the Large White and Landrace breeds, as approved by the Italian Genealogical Register, and Duroc crossbreeds. Italian pig industry for PDO hams requires heavy animals selected to have a higher amount of fat in comparison to PLOS ONE