Molecular characterization and genetic diversity analysis of aromatic rice (Oryza sativa L.) landraces using SSR markers

Abstract

The present investigation was conducted at the Department of Plant Breeding and Genetics, College of Horticulture, Vellanikkara, Thrissur and Regional Agricultural Research Station, Ambalavayal, Wayanad, The study was focused on genetic diversity among popular aromatic rice landraces using Simple Sequence Repeats (SSR) markers. Out of 86 SSR markers used for molecular characterization, 44 markers were polymorphic and remaining 42 were monomorphic. Maximum number of amplicons was exhibited by RM247 with five alleles, followed by RM85, RM251, RM248 and RM493 with four amplicons each. Among 86 SSR markers, 21 markers distinguished Basmati from traditional aromatic landraces of Wayanad viz., Gandhakasala and Jeerakasala. Seven SSR markers distinguished Gandhakasala from Jeerakasala, whereas 23 markers distinguished Basmati from Jeerakasala. Twenty-two markers distinguished Basmati from Gandhakasala and 23 markers distinguished aromatic group from non-aromatic group. Cluster analysis effectively differentiated Basmati, Jeerakasala, Gandhakasala, Uma and Aathira from each other. Among the five clusters formed, cluster III was the largest one comprising all the 12 Gandhakasala morphotypes, followed by cluster IV with all Jeerakasala morphotypes. Cluster I, Cluster II and Cluster V exhibited one genotype each namely Aathira, Uma and Basmati, respectively indicating their genetic distinctness.