The porcine HapMap projects: Genome-wide analysis of pig, wild boar and suiforme diversity and evolution

H.J. Megens, R.P.M.A. Crooijmans, G. Larson, M. Scandura, L. Iacolina, M. Apollonio, G. Bertorelle, A. Triantafyllidis, P. Alexandri, W. Muir, G. Semiadi, M. Perez-Enciso, A. Archibald, M.A.M. Groenen, L.B. Schook
8th International Symposium on Wild Boars and Other Suids, September 1-7, 2010, York, United Kingdom


The near-completion of the pig genome sequence, the availability of a genome-wide porcine, high-density SNP assay, and the introduction of next-generation sequencing technologies are currently revolutionizing the genetics of Sus scrofa and related species. The Illumina Porcine 60K SNP chip, designed by the International Suiforme Genomics Consortium (ISGC) is capable of genotyping 60,000 SNPs in a single assay. It has enabled whole-genome characterization of linkage disequilibrium and haplotype structure in commercial and local pig breeds, as part of the Porcine HapMap project, which is also coordinated by the ISGC. The Porcine HapMap project has furthermore resulted in characterization of whole-genome patterns of variation, including signatures of selection associated with domestication and breed formation, demographic events such as population bottlenecks, and the complex origin of domesticated populations by examining patterns of haplotype sharing. From the start the Porcine HapMap project sought to include non-domesticated Suidae, and the 60K assay was successfully applied to the wild boar. Currently around 2,400 individual pigs and wild boar have been successfully genotyped using the Illumina porcine 60K SNP chip. The pigs represent more than 60 distinct breeds, both local and commercial, and over 100 separate populations, from around the world. Over 600 individual wild boar were genotyped, representing more than 30 different wild boar populations distributed throughout Eurasia. In addition, museum and archaeological samples were included to provide a wider insight into domestication and geographic history. Applying the 60K assay to other Old World Suidae, including the other species in the genus Sus as well as African warthogs, bushpigs, red river hog and the enigmatic Babyrousa, allowed the estimation of the ancestral allele for most of the 60,000 SNPs, and estimation of the origin and relative age of the porcine SNPs. To further investigate the degree of sequence divergence and allele sharing between Sus scrofa and closely related species, we sequenced (Illumina GA2) the complete genomes of two island species: Sus verrucosus, occurring only on Java, and Sus celebensis, endemic to Sulawesi. A guided assembly of the genomes of these two species, based on ~7-8x genome coverage data, was done using the Sus scrofa genome, demonstrating the value of this resource for comparative suiforme genomics. Genome-wide patterns of divergence and allele sharing between these three species revealed correlation with recombination frequency and balancing vs. directional selection, and provides a framework to further investigate patterns of selection during speciation and domestication.