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.极度濒危的畜禽品种与种群常与更为常见的品种或亚种进行杂交，由此产生的遗传混杂（genetic admixture）会对野生与家养种群的遗传完整性造成威胁，进而导致特有性状或独特遗传物质的丢失，最终引发种群灭绝。为此，本研究提出两种基于全基因组DNA标记的基因组选择策略，以从混杂群体中恢复濒危原种群的基因组组成。两种策略的核心差异在于个体中非渐渗基因组比例的估算方法：其一为基因组预测法，其二为品种特异性单倍型（haplotype）鉴定法。据此可设计剔除渐渗基因组信息的育种方案。为验证上述策略，我们使用了来自两个纯种绵羊品种（美利奴羊（Merino，作为目标品种）、无角陶赛特羊（Poll Dorset））以及一个由这两个品种杂交形成的现存混杂种群的50K单核苷酸多态性（Single Nucleotide Polymorphism，SNP）阵列数据。基于这些真实基因型，我们模拟了具有不同渐渗与混杂程度的绵羊种群。两种策略均可准确识别基因组片段的来源，且均可完全剔除无角陶赛特羊的基因组片段。尽管选择过程会导致近交程度显著升高，但我们可通过限定参与下一代繁殖的个体最小数量来控制近交水平。