Analysis of single nucleotide polymorphisms in Alpine ibex using the GoatSNP50 BeadChip

The Gran Paradiso National Park is the oldest protected area in the Italian Alps and the Alpine ibex (Capra ibex ibex) is its symbol. This species, threatened with extinction at the end of the 19th century, survived only in the park. From this population, ibex was reintroduced into the European Alps. Single nucleotide polymorphisms (SNPs) are now the markers of choice for exploring genetic diversity in several species. Recently, SNP chips from livestock species have been used to identify SNPs in closely related wild species. In this study the goat 50K SNP chip was used to analyse Alpine ibex from Gran Paradiso National Park. DNA was extracted from blood samples of 8 animals sampled in the Park. Among all goat markers tested 45.966 were monomorphic and 1.329 polymorphic in the Alpine ibex. Minor Allele Frequency (MAF) distribution of polymorphic markers showed that the class that includes the highest number of markers (520) is the 0.4<MAF≤0.5 class, and that overall more than 50% of markers (860) were very informative (MAF≥0.2). Based on their genomic position in domestic goat, polymorphic loci appear distributed on all autosomes and the X chromosome. A preliminary analysis of genetic distances with domestic goat breeds reared in Northern Italy indicates that Reynold’s genetic distances between these breeds and the Alpine ibex ranged from 0.57 to 0.69, with the highest values for Orobica (0.69) and Valdostana (0.64). The high distance observed with Valdostana in our sample disagrees with the supposed introgression of Alpine Ibex in this goat breed, which is reared in the same area of the Gran Paradiso National Park. While waiting for the sequencing of C. ibex genome, this panel of 1329 goat SNPs, is the richest panel of molecular markers nowadays available for the investigation of the genetic diversity of this wild species.