Open Access Research article

Mining for single nucleotide polymorphisms in pig genome sequence data

Hindrik HD Kerstens1, Sonja Kollers2, Arun Kommadath1, Marisol del Rosario1, Bert Dibbits1, Sylvia M Kinders1, Richard P Crooijmans1 and Martien AM Groenen1*

Author Affiliations

1 Animal Breeding and Genetics Group, Wageningen University, PO Box 9101, Wageningen, 6701 BH, the Netherlands

2 IPG, Institute for Pig Genetics, PO Box 43, Beuningen, 6640 AA, the Netherlands

For all author emails, please log on.

BMC Genomics 2009, 10:4  doi:10.1186/1471-2164-10-4

Published: 6 January 2009



Single nucleotide polymorphisms (SNPs) are ideal genetic markers due to their high abundance and the highly automated way in which SNPs are detected and SNP assays are performed. The number of SNPs identified in the pig thus far is still limited.


A total of 4.8 million whole genome shotgun sequences obtained from the NCBI trace-repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project" were analysed for the presence of SNPs. Available BAC and BAC-end sequences and their naming and mapping information, all obtained from SangerInstitute FTP site, served as a rough assembly of a reference genome. In 1.2 Gb of pig genome sequence, we identified 98,151 SNPs in which one of the sequences in the alignment represented the polymorphism and 6,374 SNPs in which two sequences represent an identical polymorphism. To benchmark the SNP identification method, 163 SNPs, in which the polymorphism was represented twice in the sequence alignment, were selected and tested on a panel of three purebred boar lines and wild boar. Of these 163 in silico identified SNPs, 134 were shown to be polymorphic in our animal panel.


This SNP identification method, which mines for SNPs in publicly available porcine shotgun sequences repositories, provides thousands of high quality SNPs. Benchmarking in an animal panel showed that more than 80% of the predicted SNPs represented true genetic variation.