Exploring Genetic and Molecular Diversity of Indian Rice Landraces: A Molecular Marker-Driven Study Incorporating D2 Analysis

Abstract

Assessing genetic diversity is the key factor for enhanced crop breeding programme which aids in improving desirable characteristics in the cultivars. In the present study, 200 rice landraces were initially screened using PEG at -7 bar concentration for drought tolerance. From the 200 landraces, 12 lines with 50 % germination were chosen to assess molecular and genetic divergence. A total of 50 SSR markers were utilized across the identified 12 drought tolerant genotypes along with two susceptible and two tolerant checks to assess divergence among the genotypes. Among the 50 SSR markers, 49 exhibited polymorphisms with a PIC value ranged from 0.82 (RM447) to 0.30 (RM418) with an average of 0.63. The number of alleles varied from two (RM408, RM418, RM512) to eight (RM404) with an average of 4.4 allele per marker and a total of 216 alleles were observed. Based on unweighted pair group of arithmetic mean (UPGMA) method a dendrogram was constructed and the genotypes were grouped in four main clusters. Among the four, cluster I holding more number of genotypes than cluster IV with high dissimilarity coefficient of 0.88. Further D2 analysis for five drought traits at seedling stage revealed the similarity and diversity among the landraces by separating them in different clusters based on genetic distance. The highest inter cluster distance of 175.96 were noticed between cluster 2 and 3 with high divergence which aids in better selection of landraces. Both molecular and genetic diversity shows distinct divergence among the genotypes which exhibits broader genetic base with wider adaptability.