Exome Capture with Heterologous Enrichment in Pig (Sus scrofa)

PLoS One. 2015 Oct 2;10(10):e0139328. doi: 10.1371/journal.pone.0139328. eCollection 2015.


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 MassARRAY® system confirms that this "human-on-pig" approach offers new potentiality for the identification of DNA variants in protein-coding genes.

MeSH terms

  • Animals
  • Exome / genetics*
  • Gene Frequency / genetics
  • Gene Library
  • Introns / genetics
  • Phenotype
  • Polymorphism, Single Nucleotide / genetics*
  • Sequence Analysis, DNA / methods
  • Sus scrofa / genetics*
  • Swine / genetics*

Grant support

This research was supported by project AGER-HEPIGET: Advanced research in genomics and processing technologies for the Italian heavy pig production chain (grant N. 2011–0279). [Websites: http://www.progettoager.it; http://ager-hepiget.distal.unibo.it/.] The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The IGA Technology Services Srl was paid only for exome enrichment and DNA resequencing. The authors [SR, AS] did not receive any extra salary for the contributions reported in the 'author contributions’ section. Due to their active contribution in this study, these authors were included in the author list.