Genome-wide discovery of microsatellite markers and, population genetic diversity inferences revealed high anthropogenic pressure on endemic populations of Trillium govanianum

Abstract Trillium govanianum ethnobotanical perspectives include the treatment of cancer, hypertension, neurasthenia, giddiness, arthritis, dysentery, and inflammation. As its industrial demand for steroidal content is increasing, the endemic species have been subjected to severe habitat degradation and fragmentation by the illicit trade in Indian Himalayan Region (IHR). Additionally, molecular genetics efforts in T. govanianum has also lagged, mainly because of the non-availability of genome-wide molecular marker resources. Apropos, using tissue-specific transcriptomic data derived from the rhizome, stem, leaf, and fruit, the present study identified 5337 novel functionally relevant genome-wide SSR markers. The tri repeats were most abundant (41%) with a higher occurrence of CCG/CGG repeat motif, mostly located in the CDS region. Based on functional annotations of SSR transcripts with multifarious public databases (NR, TAIR, KEGG, KOG, SwissProt & PTFdb), a set of 288 SSR markers encompassing important roles in steroidal saponins pathway, cellular and metabolic processes such as response to stress, binding, and catalytic activity were validated, successfully. Genetic diversity and population structure analysis of 290 genotypes of 14 geographically distinct populations representing eight different valleys (2086−3500 m amsl) of the IHR amplified an average of 4.33 alleles per locus. Overall, a low genetic diversity (He: 0.25), high genetic divergence (GST: 0.23), high within populations molecular variance (72 %), limited gene flow (0.792), and slight positive isolation by distance (Rxy = 0.260; p = 0.030) is recorded in T. govanianum populations. Further, neighbor-joining (NJ) based hierarchical clustering, PCoA, and Bayesian structure clustering identified two major groups in the tested populations. Novel microsatellite marker resources and population diversity inferences studied for the first time revealed that there is a need to recuperate diversity in situ and maintain effective population size, a much-required step to mitigate high anthropogenic pressure on T. govanianum in Indian Himalayan Region.