Understanding the genetic diversity and population structure of Dendrobium chrysotoxum Lindl.-An endangered medicinal orchid and implication for its conservation

Abstract

Genetic variation study in 11 populations of D. chrysotoxum was conducted using 20 different inter-simple sequence repeats (ISSR) and 9 start codon targeted (SCoT) primers. Out of 199 bands produced by ISSR markers, 196 bands were polymorphic, resulting in high polymorphism (98.49%). SCoT markers, however, produced 111 polymorphic fragments generating 100% polymorphism. The Nei's genetic diversity at the species level (H = 0.184±0.11 for ISSR; H = 0.236±0.12 for SCoT) was higher than the average value at the population level (H = 0.160±0.15 for ISSR; H = 0.174±0.15 for SCoT). Low genetic differentiation among the populations (Gst = 0.1566 for ISSR; Gst = 0.2677 for SCoT) was observed due to high estimate of gene flow (Nm = 2.6938 for ISSR; Nm = 1.3678 for SCoT). Mantel test revealed a non-significant correlation between the genetic and geographical distance (r = -0.62; p = 0.86 for ISSR; r = -0.68; p = 0.82 for SCoT). Two-dimensional principal coordinate analysis (PCoA) determined the contribution of the first two principal components to the total genetic variation for combined ISSR and SCoT data at 13.71%. The distribution of individuals in the PCoA plot was in accordance with the unweighted pair group method with arithmetic averages (UPGMA) cluster analysis. Bayesian model-based STRUCTURE determined three (K = 3) gene pools for both ISSR and SCoT markers with a high degree of admixture in the populations. GENELAND further assigned the 11 different populations into 7 genetic clusters. Based on the genetic information obtained from the present investigation, we recommended different conservation strategies suited for effectively managing the endangered orchid. To the best of our knowledge, this is the first report of estimating the genetic diversity and population genetic structure of D. chrysotoxum in Manipur, a north-eastern state of India bordering Myanmar.