Morphological and molecular markers based assessment of genetic diversity of a valuable endemic plant Lasiurus sindicus Henr. in the arid region of Rajasthan, India

Abstract Morphological and molecular markers are useful in genetic diversity assessment and improvement of plants. In the present study, five morphological traits, random amplified polymorphic DNA (RAPD) and Start codon targeted (SCoT) markers were used for genetic diversity evaluation of Sewan grass (Lasiurus sindicus Henr.), a valuable endemic plant of Indian Thar desert. Accessions collected from 14 different sites were used for measuring morphological traits, namely plant height (PH), number of tillers (NT), number of nodes (NN), leaf length (LL) and spike length (SL) which showed large variations among populations; particularly PH, NT and LL. Ward’s linkage hierarchical cluster analysis exhibited two major clusters and Cluster I contained two minor clusters. The percentage polymorphic bands (PPB) produced were 89.64% and 64.51% for RAPD and SCoT respectively. RAPD markers based dendrogram revealed three clades while there was no clear clade formation with SCoT markers. Single primer amplification reaction (SPAR) analysis with combined data of RAPD + SCoT showed more similarity with SCoT than with RAPD clusters. AMOVA revealed higher variation within population (90%) than among populations (10%) of L. sindicus. The Principal coordinate analysis (PCoA) also supported this result. There was no correlation between morphological and molecular data confirming environmental impact on morphological variation. SCoT and SPAR markers have clearly identified a novel genotype (LS JS 3) which has high values of PH, NN and LL. This study suggests that morphological data combined with molecular data can alone help in the identification of novel genotypes of L. sindicus among its populations.