A new livestock multispecies SNP array to characterize genomic variation in European livestock gene bank collections

Molecular genetic characterization of genetic resources is essential to study biodiversity. Whereas whole genome sequencing is still relatively expensive, low density SNP arrays offer a cost-effective and standardized solution. However, most of the current arrays are species specific. Their high SNP density often exceeds diversity mapping requirements and remains too costly for many genetic resource managers. The IMAGE H2020 project aimed at developing a low-cost multispecies SNP array to facilitate mapping of the genetic diversity in samples stored in gene banks and in vivo (on farm) traditional populations. This farm animal multispecies array contains approximately 10 K SNPs per species. The species included are cattle, sheep, goat, horse, pig, and chicken. We developed and tested this array on many samples from each of the six species. We describe here the SNP coverage and informativity across 253 breeds. We show that the array can be used to cluster local breeds according to history and genetic diversity. We illustrate its use for parentage testing. The array is publicly available at a reasonable price if ordered in multiples of 384 samples, leading to an overall cost of genotyping of approximately 15 euros per sample.