Towards a genomic platform for analysis of wild boar and suiforme diversity and evolution

R. Crooijmans, T. Baxter, S. Casu, K. Chen, A. Ducos, S. Genini, E Guiffra, U.T. Ju, H.P. Koelewijn, M. Longeri, E. Luetkemeier, R. Malhi, H.J. Megens, W. Muir, N. Okumura, M. Perez-Encisco, A. Roca, C. Roseman, G. Semaidi, M. Sodhi, G. Larson, M Groenen, L. Schook
7th International Symposium on Wild Boar (Sus Scrofa) and Sub-Order Suiformes, August 29, 2008, Sopron, Hungary


Archaeological evidence indicates that the pig (Sus scrofa domesticus) was definitively domesticated from the wild boar (Sus scrofa) in the Near East approximately 9,000 years ago. Studies utilizing mitochondrial DNA derived from modern and ancient wild and domestic pigs indicate several other regionally and genetically distinct pigs were likely independently domesticated in Central Europe, Italy, Northern India, East Asia, and Peninsular Southeast Asia. Our efforts are focusing on the use of genomic DNA polymorphisms (single nucleotide polymorphisms, SNPs) to assess nuclear variability within global wild boar and domestic pig populations.  Our goals are to provide a genomics platform to: 1) define wild boar and domestic populations; 2) define the evolution of Sus scrofa and suiformes; and 3) assist captive breeding (including traceability) and management projects. The pig genome sequencing project provides a reference sequence to support SNPdiscovery. The International Suiforme Genomics Consortium (ISGC) is focusing on SNP discovery using global wild boar (35 samples from Europe and Asia) and ten European, North American and Asian domesticated breeds. Reduced representation libraries (RRL) were constructed from this diverse germplasm and sequenced using Solexa and 454 platforms and SNPs were incorporated into a bioinformatics platform for identification of SNPs with > 0.10 minor allele frequencies covering the complete pig genome. These SNPs were subsequently used by the ISGC to design an Illumina iSelect pig DNA chip (60,000 SNPs).  This pig SNP chip will be used to define wild boar and domesticated populations. The knowledge gained from inclusion of wild boar and outgroup populations will be of tremendous value for interpreting SNP variation in the domesticated pig through the inference of ancestral derived alleles and coalescent patterns across the genome. The ISGC welcomes new members to provide broader access to germplasm and to assist in further defining the wild  origins and related suiformes.