Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-550) contains supplementary material, which is available to authorized users.
Highlights
The domestic pig (Sus scrofa) is both an important livestock species and a model for biomedical research
Approximately 85% of known disease-causing mutations can be found within the coding region or splice sites of protein-coding genes [3]. Whilst this number may be biased by studies focused only on protein-coding genes, exome sequencing has become a standard tool in the search for the cause of monogenic disorders in humans [3,4,5,6,7]
Definition of the capture region The exons of protein coding genes from release 71 of the Ensembl genebuild for Sus scrofa sum to a total length of 44.6 Mb, compared to 73.4 Mb for human and 67.1 Mb for mouse (Figure 1)
Summary
The domestic pig (Sus scrofa) is both an important livestock species and a model for biomedical research. Approximately 85% of known disease-causing mutations can be found within the coding region or splice sites of protein-coding genes [3]. Whilst this number may be biased by studies focused only on protein-coding genes, exome sequencing has become a standard tool in the search for the cause of monogenic disorders in humans [3,4,5,6,7]. Whereas many quantitative traits are linked to variation in gene expression, the initial sequencing of the pig genome revealed that individual pigs harbour significant numbers of potentially deleterious protein-coding mutations [12]
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