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Open Access Highly Accessed Research article

Design and development of exome capture sequencing for the domestic pig (Sus scrofa)

Christelle Robert1, Pablo Fuentes-Utrilla12, Karen Troup12, Julia Loecherbach12, Frances Turner12, Richard Talbot12, Alan L Archibald1, Alan Mileham3, Nader Deeb4, David A Hume1 and Mick Watson12*

Author Affiliations

1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK

2 Edinburgh Genomics, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK

3 Genus plc, 1525 River Road, DeForest, WI 53532, USA

4 Genus plc, 100 Bluegrass Commons Blvd. Suite 2200, Hendersonville, TN 37075, USA

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BMC Genomics 2014, 15:550  doi:10.1186/1471-2164-15-550

Published: 3 July 2014

Abstract

Background

The domestic pig (Sus scrofa) is both an important livestock species and a model for biomedical research. Exome sequencing has accelerated identification of protein-coding variants underlying phenotypic traits in human and mouse. We aimed to develop and validate a similar resource for the pig.

Results

We developed probe sets to capture pig exonic sequences based upon the current Ensembl pig gene annotation supplemented with mapped expressed sequence tags (ESTs) and demonstrated proof-of-principle capture and sequencing of the pig exome in 96 pigs, encompassing 24 capture experiments. For most of the samples at least 10x sequence coverage was achieved for more than 90% of the target bases. Bioinformatic analysis of the data revealed over 236,000 high confidence predicted SNPs and over 28,000 predicted indels.

Conclusions

We have achieved coverage statistics similar to those seen with commercially available human and mouse exome kits. Exome capture in pigs provides a tool to identify coding region variation associated with production traits, including loss of function mutations which may explain embryonic and neonatal losses, and to improve genomic assemblies in the vicinity of protein coding genes in the pig.