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Hybridization between wild boar (Sus scrofa) and their domestic relative, pigs, is a global issue and gene flow between these populations has been known to negatively impact biodiversity with increased aggression, litter sizes, and growth. However, establishing a cost-effective analysis for long-term monitoring of possible gene flow of wild pigs into wild boar populations is challenging due to common alleles at multiple loci and often it is difficult to distinguish boar specific lineages. Therefore, there is a need to select loci with lineage specific alleles for hybrid detection. To determine these loci, we calculated allele frequencies and measurements from successfully amplified loci with DNA extracted from domestic pigs and wild boar populations from the period prior to, and after, the evacuations and disasters in Fukushima, Japan, in 2011, which resulted in an uncontrolled release of domestic pigs. Thirty-two loci showed pig putative alleles suggesting these selected loci can be useful genetic markers. Seventeen loci successfully distinguished pig and wild boar hybridization in Fukushima populations. Identified loci from this study provide a cost-efficient tool for genetic analysis and will provide a wealth of information on how an uncontrolled release of domestic livestock from natural or disasters may impact their wild relatives.
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