Ginger (Zingiber officinale) is grown worldwide in subtropical and tropical regions and primarily used as a spice and medicinal plant. Despite the economic importance of ginger, research on its molecular aspects is limited. Moreover, although ginger is mainly cultivated through vegetative propagation owing to poor flowering and infertility, few molecular markers have been identified to distinguish cultivars. In this research, we developed five Cleaved Amplified Polymorphic Sequence (CAPS) markers that can distinguish between the “Bongdong” ginger (Bg) cultivar, indigenous to South Korea, and the Chinese imported ginger (Cg) cultivar through reference sequencing based on the recently reported complete genome information of ginger. Furthermore, the integrated application of the five CAPS markers allow us to distinguish between Bg, Cg, and Indonesian ginger. Among them, the ClaI-based CAPS marker was identified as specific to Bg cultivars. Therefore, TaqMan real-time PCR based on ClaI-based CAPS can be widely used to distinguish between Bg and Cg cultivars. This study is the first to report the development of genome-based single-nucleotide polymorphism markers in ginger and therefore provides important information for the breeding and conservation of ginger.

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