Developing Novel Microsatellite Markers for Kaempferia parviflora by Microsatellite Capture Sequencing (MiCAPs)

Kaempferia parviflora, a medicinal plant widely used in Southeast Asia, has been validated clinically for its diverse pharmaceutical applications. Despite extensive research in pharmacology, there is a notable lack of cytogenetic and genomic research, primarily due to limited genetic information. Simple Sequence Repeat (SSR) is considered a robust class of molecular markers frequently used in biodiversity studies. In this study, we adopted Microsatellite Capture Sequencing (MiCAPs) to obtain SSR sequences for marker development. We identified 13,644 SSRs and developed and validated ten sets of SSR markers through capillary electrophoresis. The ten primer sets generated 27 alleles, with an average Polymorphism Information Content (PIC) of 0.36. Principle Coordinate Analysis (PCoA) distinguished two types of K. parviflora, consistent with classification by leaf margin color (red and green). A neighbor-joining dendrogram of seven Zingiberaceae species was constructed with the SSR-containing sequences. The 2-c value of K. parviflora is first reported here as 3.16 ± 0.03; the genome size is estimated at 3090.48 Mbp. The newly developed molecular markers are crucial for variety identification and the conservation of wild resources. Additionally, the cytogenetic and phylogenetic information provides valuable insights into the genetic diversity and evolutionary relationships.