Assessing Genetic Diversity in Endangered Plant Orchidantha chinensis: Chloroplast Genome Assembly and Simple Sequence Repeat Marker-Based Evaluation

<i>Orchidantha chinensis</i> T. L. Wu, an endemic species in China, is listed as a key protected wild plant in Guangdong Province. However, the lack of reports on the chloroplast genome and simple sequence repeat (SSR) markers has hindered the assessment of its genetic diversity and conservation strategies. The limited number of molecular markers to assess the genetic diversity of this species, and thus develop proper conservation strategies, highlighted the urgent need to develop new ones. This study developed new SSR markers and investigated genetic variation using 96 samples of <i>O. chinensis</i> from seven populations. Through high-throughput sequencing, a complete chloroplast genome of 134,407 bp was assembled. A maximum-likelihood phylogenetic tree, based on the chloroplast genome, showed that <i>O. chinensis</i> is closely related to <i>Ravenala madagascariensis</i>. The study identified 52 chloroplast SSRs (cpSSRs) and 5094 expressed sequence tag SSRs (EST-SSRs) loci from the chloroplast genome and leaf transcriptome, respectively. Twenty-one polymorphic SSRs (seven cpSSRs and fourteen EST-SSRs) were selected to evaluate the genetic variation in 96 accessions across seven populations. Among these markers, one cpSSR and 11 EST-SSRs had high polymorphism information content (>0.5). Cluster, principal coordinate, and genetic structure analyses indicated that groups G1 and G6 were distinct from the other five groups. However, an analysis of molecular variance showed greater variation within groups than among groups. The genetic distance among the populations was significantly positively correlated with geographical distance. These findings provide new markers for studying the genetic variability of <i>O. chinensis</i> and offer a theoretical foundation for its conservation strategies.