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

Abstract

The pig (Sus scrofa domesticus) was domesticated from Sus scrofa, the wild boar, 9,000 years ago and studies utilizing mitochrondrial DNA analysis indicate that this occurred through multiple independent events around the world (Central Europe, Italy, Northern India, South East Asia, and Island Southeast Asia). Our efforts are focusing on the use of genomic DNA polymophisms (single nucleotide polymorphisms, SNPs) to assess nuclear contributions to global wild boar and domestic populations. Our goals are to provide a genomics platform that can be used to: 1) define wild boar and domestic populations; 2) define the evolution of Sus scrofa and suiformes; and 3) provide a tool to assist in captive breeding and management projects. The pig genome sequencing project provides a reference sequence to support SNP discovery and next generation re-sequencing projects. This International Suiforme Genomics Consortium (ISGC) is thus focusing on SNP discovery using global wild boar germplasms (35 samples from Europe and Asia) and ten European, North American and Asian domesticated breeds. Reduced representation libraries (RRL) have been constructed from this diverse germplasm. These RRL were 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 a high density Illumina iSelect pig DNA chip (60,000 SNPs). This pig SNP chip will be used to define wild boar and domesticated populations and to determine its utility in captive breeding and management programs. The ISGC welcomes new members to provide broader access to germplasm and to assist in further defining the wild origins and related suiformes