Microsatellite marker resource, genetic diversity, bottleneck, and expected habitat inferences for conservation of critically endangered Saussurea costus (Falc.) Lipsch

Abstract

Saussurea costus (Falc.) is an important medicinal herb known to treat diverse medical ailments that require an immediate conservation effort to rescue its natural genetic resources. This study aimed to implement an integrative use of molecular and climatic data to assess population genetics, genetic structure, and habitat suitability providing comprehensive insights to facilitate conservation strategies. The phylogenetic analysis using 701 orthologous groups of 26 representative plant species revealed a close evolutionary relationship between S. costus and A. lappa. Furthermore, transcriptome-derived 17,022 SSR marker resource was created and a set of informative markers were utilized for the genotyping of 215 individuals comprising 17 populations, which revealed compromised genetic diversity (Ho = 0.24), significant inbreeding (Fis = 0.48), and higher population differentiation (Fst = 0.28). AMOVA exhibited 29 % variation among populations and STRUCTURE, PCoA, and UNJ clustered populations into three gene pools predominantly structured by geographic isolation. Besides, a strong genetic structure and isolation by distance, the genetic bottleneck reported a significant reduction in 13 of the 17 tested populations of S. costus. Additionally, habitat suitability is predicted to deteriorate in at least 64 % of the area in future. Nevertheless, populations with high genetic diversity and climatic hotspots may provide valuable germplasm with suitable geographical regions to evolve strategies for conservation and sustainable utilization of S. costus. In future, identified core genotypes and functionally relevant SSR marker resource created in this study can be utilized to implement molecular breeding efforts for genetic improvement and selection of elite cultivars for commercial cultivation.