To monitor and control the Japanese orange fly Bactrocera tsuneonis, it is important to determine their dispersal ability. Therefore, to determine the genetic structure of this species, we developed microsatellite markers at 17 loci for B. tsuneonis. A total of 80 adult females and males randomly collected from abandoned orchards in the Oita and Yamaguchi Prefectures, in the western part of Japan, were used for polymorphism analysis using the microsatellite markers. The average number of alleles was 2.65 for the 17 loci, in which two loci did not show polymorphism. The expected heterozygosity ranged from 0 to 0.663, although the observed heterozygosity was relatively low between 0-0.105. The null allele frequencies varied among populations. Moreover, no polymorphism was found in the three larval populations collected in the Oita Prefecture. These results suggested a high degree of inbreeding for this species. Significant genetic differentiation between females and males of the same population was not observed, although it was observed between the Oita and Yamaguchi populations.A bottleneck effect was detected in Yamaguchi but not in Oita, and this is congruent with the history of an expanding distribution in this species. These markers could be used for population discrimination and to expand the geographic history of this species, potentially contributing to the pest management of B. tsuneonis.
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