Microsatellite loci were developed for Gynochthodes boninensis, an endemic climbing plant in the Bonin Islands. Using a Roche 454 GS Junior next-generation sequencer, 158 microsatellite loci were designed. Of the 48 microsatellite loci tested, 37 were successfully amplified and 25 were polymorphic in two populations of G. boninensis. For the 25 polymorphic loci, the mean expected heterozygosities per locus were 0.303 in the Chichijima Island population and 0.310 in the Hahajima Island population, respectively. There was no evidence of linkage disequilibrium in either population, but one locus showed significant deviation from Hardy–Weinberg equilibrium in one population. The microsatellite loci developed in this study will be useful for future studies of population genetics of G. boninensis. In particular, because this species is androdioecious (males and hermaphrodites coexist), characterizing the species gene flow is crucial to understanding the evolution and maintenance of this rare sexual system.
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