Comprehensive SSR study of 14 Zingiberaceae species based on Microsatellite Capture Sequencing (MiCAPs)

MiCAPs was applied to 160 accessions, including 148 individuals from 14 Zingiberaceae species and 12 outgroup samples (Musaceae), generating 21.78 million raw reads. From this dataset, 612 SSR marker candidates were developed and evaluated via electronic-PCR (ePCR) for seven target species. A phylogenetic tree reconstructing the relationships among the 14 Zingiberaceae species was successfully constructed using the consensus sequence from MiCAPs data. Furthermore, the distribution of species-specific and transferable SSR loci was assessed across the Curcuma or Zingiber species using Polymorphic SSR Retrieval (PSR) analysis. Comparative genetic diversity studies focusing on the Curcuma and Zingiber genera revealed that Zingiber exhibits a relatively more conserved genetic background compared to Curcuma.