Data from: Genomic selection for recovery of original genetic background from hybrids of endangered and common breeds

Critically endangered breeds and populations are often crossed with more
common breeds or subspecies. This results in genetic admixture that can be
undesirable when it challenges the genetic integrity of wild and domestic
populations, causing a loss in special characteristics or unique genetic
material and ultimately extinction. Here, we present two genomic selection
strategies, using genome-wide DNA markers, to recover the genomic content
of the original endangered population from admixtures. Each strategy
relies on the estimation of the proportion of nonintrogressed genome in
individuals based on a different method: either genomic prediction or
identification of breed-specific haplotypes. Then, breeding programs that
remove introgressed genomic information can be designed. To test these
strategies, we used empirical 50K SNP array data from two pure sheep
breeds, Merino (used as target breed), Poll Dorset and an existing admixed
population of both breeds. Sheep populations with varying degrees of
introgression and admixture were simulated starting from these real
genotypes. Both strategies were capable of identifying segment origin, and
both removed up to the 100% of the Poll Dorset segments. While the
selection process led to substantial inbreeding, we controlled it by
imposing a minimum number of individuals contributing to the next
generation.