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

Abstract

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.

Keywords: de-introgression; original background recovery; undesired introgression.

Figure 1

Diagram of the introgression simulation. The real individuals were used to create a mixed population of 100 individuals that mated randomly during one to five generations. Next, five generations of management started.

Figure 2

Plot of the 549 haplotypes origin of chromosome 1 in a sample of 25 random pure Merino, 25 random pure Poll Dorset and 25 random crossed animals. Each line represents an individual's chromosome.

Figure 3

Comparison of the GBLUP solutions and the haplotypes results. The GBLUP solutions are represented on the vertical axis and the mean b values per individual from the haplotype approach on the horizontal axis.

Figure 4

Proportion of Merino recovered (upper panels) after one or five generations of management and ΔF (lower panels) after one or five (cumulative ΔF) generations of management using the haplotype approach, for one, three or five generations of admixture (20 individuals contributing).

Figure 5

Proportion of Merino recovered (upper panels) after one or five generations of management and ΔF (lower panels) after one or five (cumulative ΔF) generations of management using the haplotype approach for five or 20 generations of admixture (40 individuals contributing).