Detecting interspecific hybridization with Illumina SNP BeadChips: A case study based on the Spanish ibex

Single nucleotide polymorphism (SNP) arrays allowing to characterize the genome-wide diversity of domestic species have been developed in the last decade. Herewith, we aim to assess the applicability of the Goat SNP50 BeadChip to detect the introgression of Iberian wild goats (Capra pyrenaica) with domestic goats (Capra hircus). By genotyping 118 Iberian wild goats, we have found that as much as 21,621 caprine SNPs (40.54% of all SNPs contained in the goat chip) segregate in the Iberian wild goat population (MAF > 0.01). This extensive sharing of polymorphic markers was due to the presence of eight Iberian wild goats from Tortosa-Beceite showing signs of domestic goat introgression. Information provided by the chip made possible to demonstrate that genomic segments containing introgressed SNPs were enriched in genes related with the immune and neuronal systems. Moreover, we have surveyed the genetic variation of Iberian wild goats by sequencing. This experiment yielded a data set of 5.08 million SNPs that can be accessed at Figshare database. Only 4.69% of these SNPs were also present in a SNP data set generated from 40 domestic goat whole-genome sequences. The main conclusion that can be derived from our study is that massive SNP arrays are an excellent tool to survey, at a large-scale and with a modest economic cost, the introgression of wild species with their domestic counterparts. The application of this tool to the study of Iberian wild goat diversity has demonstrated that introgression with domestic goats is not widespread.