ABSTRACT
Aim: The present study was undertaken to analyze the extent of genetic variability existing among twenty accessions of Lawsonia inermis, collected from Rajasthan and Gujarat states of India, using gene targeted SCoT, arbitrarily amplified ISSR and nuclear rDNA markers. Methodology: Twenty henna accessions, vegetatively established at the Institute were collected from Rajasthan (7) and Gujarat (13). Twenty-six SCoT and twenty ISSR markers generating distinct, unambiguous and scorable fragments were selected, after preliminary screening for assessment of genetic diversity. Data analysis was performed using NTSYS-pc, GenAlEx 6 and POPGENE version 1.31 programs, and dendrograms were generated using unweighted pair group method for arithmetic mean (UPGMA). The internal transcribed spacer (ITS) region of ribosomal DNA was amplified using universal primers followed by sequencing and dendrogram generation. Results: SCoT markers revealed lower values of similarity coefficients ranging from 0.87 - 0.93 compared to 0.93 - 0.98 for ISSR. SCoT markers delineated the L. inermis cultivars into three distinct clusters while ISSR markers demarcated them into five clusters. Interpretation: The Gujarat population of L. inermis was richer in genetic diversity than that of Rajasthan. SCoT markers proved better than the ISSR markers for genetic diversity analysis. Substantial variation in ITS-1 region due to SNPs, INDELS and ITS length polymorphism the nucleotide sequences signified its phylogenetic utility in assessing genetic diversity in of L. inermis.