The porcine HapMap project: Genome-wide assessment of nucleotide diversity, haplotype diversity and footprints of selection in the pig

M.A.M. Groenen, A. Amaral, H.J. Megens, G. Larson, A.L. Archibald, W.N. Muir, R. Malhi, R.P.M.A. Crooijmans, L. Ferretti, M. Perez-Encizo, L.B. Schook
Plant and Animal Genome XVIII Conference, January 10-14, 2010, San Diego, CA


The pig has a complex and long history of domestication and breed formation and has been domesticated independently multiple times and has likely experienced introgression of local Wild boar after the spread of agriculture. Using the Illumina GA sequencing platform thousand s of SNPs were identified in the porcine genome and used these to develop the Illumin porcine 60K iSelect Beadchip. This chip has enabled whole-genome characterization of linkage disequilibrium and haplotype structure in commercial and local breeds and comparison with the Wild boar. The chip has also allowed an investigation into whole-genome patterns of variation, including signatures of selection associated with domestication and breed formation as well as elucidating demographic events such as population bottlenecks, and providing insights into the complex origin of domesticated populations by examining patterns of haplotype sharing. Signatures of selection were also identified using Illumina short read sequences generated from pooled reduced representation libraries of different breeds and covering approximately 2% of the genome. Signals of positive selection were identified and a GO term/KEGG pathway enrichment analysis provided evidence for specific gene families under selection in domesticated pigs and Wild boar. Currently approximately 2,000 pigs were been genotyped with the porcine 60K beadchip, including approximatley 50 pig breeds, and about 20 different Wild boar populations distributed throughout Eurasia. In addition, museum and archeological samples were included to provide a wider insight into domestication and geographic history. Inclusion of a range of other Suidae as outgroup species, supported an estimation of ancestral alleles and the origin and relative age of the porcine SNPs.