Unplanned crossbreeding between a native livestock and a specific productive breed was one of the main reasons that caused the loss of valuable genetic resources in native livestock. To avoid further loss and damage of genetic resources in the native livestock, introgressed individuals should be distinguished to eliminate them by preventing any further employment in future mating plans. In general, the genetic diversity of native livestock had already decreased and mass elimination of introgressed individuals from the population endangers their existence. To solve this problem, high-resolution markers are required to discriminate between introgressed variation and native variation. Here, we applied ddRAD-Seq markers for native Japanese horse \"Taishu\" that has undergone recent genetic introgression. Genome-wide ddRAD-Seq markers can distinguish five breeds of native Japanese horses and Anglo-Arabian introgressed breeds. We found the signatures of genetic introgression of Anglo-Arabian at only two chromosomes; however, the signatures were separated in their genome suggesting that it might not be the cause of recent introgression. The genetic diversity of Taishu was less than other Japanese breeds and the decreasing genetic diversity is an urgent issue compared to genetic introgression. Although few signatures of recent introgression were detected, a lot of shared SNPs (10% of all SNPs in Taishu) were detected between Taishu and Anglo-Arabian. To avoid misestimation of the presence and degree of introgression in native livestock, information regarding shared SNPs and population genetic approaches need to be assessed by using the large number of genome-wide markers such as ddRAD-Seq.
