To estimate the degree of crossbreeding between Japanese wild boars and crossbred Inobuta in Wakayama prefecture, we examined haplotypes of mitochondrial DNA (mtDNA) and genotypes of the nuclear glucosephosphate isomerase-processed pseudogene (GPIP) in tissue samples obtained from 176 wild boars over a 3-year period. Five different haplotypes (J10, J15, J21, J22 and J23) and 3 GPIP alleles (GPIP1, GPIP3a and GPIP3b) were detected. These genetic profiles were classified as Japanese wild boar lineage without the genetic markers typical of Inobuta. The present genetic profile of wild boars, consisting of mtDNA haplotypes and GPIP genotypes, is a useful tool for studying the genetic structure of the local feral population.
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