Whole genome re-sequencing of pigs and wild boar reveals unexpected signatures in variation related to biogeography, domestication, and hybridization

H.J. Megens, G. Larsor, R. Crooijmans, L. Andersson, C.J. Rubin, L. Frantz, L.B. Schook, and M. Groenen
Plant and Animal Genome XX Conference, January 14-18, 2012, San Diego, CA


In pigs (Sus scrofa), haplotype analysis, particularly mtDNA, and more recently the Y chromosome, has led to a number of important discoveries regarding biogeography and domestication of the species. While such analyses have been important for ascertaining domestication and hybridization events, they have not provided good estimates for the degree of hybridization, and, in addition, generally provide poor biogeographic signals. Sequencing entire genomes of pigs and wild boar throughout the range of the species can reveal a treasure trove of haplotype information, with those regions in the genome with relatively low levels of recombination potentially being most useful for this purpose. Here we present an analysis based on whole genome resequencing data of 55 pigs, wild boar, and outgroup species. The analysis revealed hitherto unknown biogeograpic relationships between northern Eurasian populations of wild boar. Furthermore, we investigated a complex pattern of domestication in Chinese pigs, and found evidence for recent introgression from Western pigs. Lastly, we investigated evidence for the historic introgression from Eastern pigs into Europe in the 18th, 19th century. The distribution of genomic haplotypes could be corroborated by applying high-density genotype data derived from around 2000 pigs and wild boar (60K Porcine Illumina BeadArray).