Genetic diversity and population structure of the endangered medicinal plant Ferula sinkiangensis

Ferula sinkiangensis, an endangered medicinal plant of the Apiaceae family, is endemic to the arid region of the Ili Valley in the Xinjiang Autonomous Region of China. F. sinkiangensis holds significant economic, edible and therapeutic value. However, because of its small population size and limited geographic range, F. sinkiangensis faces serious risks, highlighting its critical importance and urgent need for conservation. Moreover, genetic boundaries between F. sinkiangensis and its widespread congener F. feruloides still remain unclear. In this study, we employed restriction site-associated DNA sequencing (RAD-seq) to analyze the genetic diversity, population structure, and demographic history of F. sinkinagensis using 61,344 SNPs obtained from 229 individuals sampled within the distribution area of F. sinkiangensis (150) and F. feruloides (79), respectively. Our findings indicate that F. sinkiangensis has intermediate-level genetic diversity (pi = 0.086, HO = 0.089, HE = 0.086) while F. feruloides shows higher genetic diversity (pi = 0.116, HO = 0.126, HE = 0.107). Population genomic analyses, including STRUCTURE and principal components analysis (PCA), revealed that F. sinkiangensis constitutes a distinct genetic cluster. Complementary analyses, such as phylogenetic tree construction, further support the finding that F. sinkiangensis and F. feruloides form two separate genetic clusters. Furthermore, analysis of F. sinkiangensis alone displayed two subpopulations. Together, these results underscore the unique genetic identity of F. sinkiangensis within its phylogenetic context. Both species exhibited similar demographic histories from the period prior to the Last Glacial Maximum (LGM) through the Inter-glacial period. During the Inter-glacial period, populations experienced fluctuations in size, followed by a recovery in effective population size after the LGM. Our population genetic analyses of F. sinkiangensis establish a baseline for future conservation efforts and reveal that recent population declines are linked to external human activities over the past few decades. These findings underscore the urgent need for conservation efforts that employ both in-situ and ex-situ approaches to conserve F. sinkiangensis.