Exploring the genetic diversity and population structure of Bacopa monnieri (L.) using random amplified (RAPD and ISSR) and gene-targeted (SCoT and CBDP) markers

Bacopa monnieri is an ancient herb and traditional ayurvedic medicine used as a nerve tonic and enhances memory. To improve the taxonomic authentication and evolutionary relationship, the genetic variation of this herb was studied using arbitrary amplified (Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeats (ISSR)), gene-targeted (Start codon targeted (SCoT) polymorphism (SCoT), and CAAT box-derived polymorphism (CBDP) markers. A total of 30 accessions were collected from 14 states of India. The polymorphic information content of RAPD, ISSR, SCoT, and CBDP markers were 0.315, 0.345, 0.34, and 0.38 per primer respectively. The Resolving power of RAPD, ISSR, SCoT, and CBDP markers were 6.16, 6.97, 1.62, and 4.62 per primer respectively. Unweighted pair group method with arithmetic mean (UPGMA) based Phylogenetic tree clustered the 30 Bacopa accessions into three clusters. IC-284992 and IC392842 from Odisha were found together in one cluster with all four marker systems depicting their genetic similarity. Population structure-based analysis divided the genotypes into two, four, three, and two populations with RAPD, ISSR, SCoT, and CBDP markers, respectively. Substantial genetic differentiation was observed with all set of markers with their Fst values for RAPD, ISSR, SCoT and CBDP being 0.348, 0.677, 0.687, 0.404 respectively, showing good amount of genetic diversity among the accessions. This study shows that gene-targeted markers (SCoT and CBDP) are more efficient than Arbitrarily Amplified DNA markers (AAD) markers for detecting polymorphism in Bacopa and can be used in its germplasm exploration, utilization, and management.