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.