ArticleScientific reports2026
Investigating the genetic potential of Ashwagandha (Withania somnifera L. Dunal) germplasm through SCoT and EST-SSR molecular markers.
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Abstract
Ashwagandha (Withania somnifera L. Dunal) is a highly acclaimed medicinal herb belonging to the family Solanaceae. The plant has been rendered an essential component of the Indian medicinal system due to its high therapeutic potential, attributed to its rich profile of secondary metabolites, namely withanolides. Widespread cultivation of the herb across diverse agroclimatic conditions has resulted in the development of numerous varieties and landraces, making it very difficult to discriminate the elite germplasm using conventional approaches. To overcome these, we use two molecular marker systems, SCoT and EST-SSR, to study the genetic variation and population structure of 32 Withania accessions. A total of 113 and 26 reproducible bands were generated using 10 SCoT and 17 EST-SSR markers, respectively, of which 100 and 20 were polymorphic, with an average polymorphism rate of 88 and 85.3%. The mean polymorphism information content (PIC), Marker Index (MI), and Resolving Power (Rp) for SCoT and EST-SSR markers were 0.327 and 0.172, 2.98 and 0.282, and 7.24 and 1.14, respectively, indicating that SCoT markers are more informative than EST-SSR markers for genetic diversity assessment. Cluster analysis using Jaccard similarity coefficients revealed distinct genetic groupings: SCoT markers formed two clusters, and EST-SSR markers formed two main clusters, with some outliers. Population structure analysis using Bayesian clustering revealed two ancestral populations with high admixture. This is the first time SCoT markers were used to assess genetic diversity in Withania somnifera. Quantitative real-time (qRT-PCR) expression analysis of six withanolide biosynthetic pathway genes (GT, CAS, FPPS, HMGR, SE, SS) across four genotypes of Withania somnifera reveals genotype-specific differential expression, further supporting the diversity observed by molecular markers. Our results indicate that both markers are informative and can be used to detect distinct genetic variations within Withania genotypes, providing valuable insights for breeding and conservation efforts and enabling the development of improved cultivars suited to various agroclimatic conditions.
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