Genetic polymorphism in rice (Oryza sativa L.) through RAPD analysis

Random Amplified Polymorphic DNA (RAPD) assay was performed to estimate genetic polymorphism in six different rice (Oryza sativa L.) cultivars viz. Basmati 370, DM 25, IRATOM 24, Binadhan 6, TNDB 100 and Y 1281. Three out of the 15 decamer random primers showed amplification of genomic DNA in 24 individuals. The primers produced a total of 26 bands of which 14 were polymorphic. Proportion of polymorphic bands and gene diversity estimates were 26.92% and 0.09 for Basmati 370, 11.54% and 0.04 for DM 25, 11.54% and 0.05 for IRATOM 24, 7.69% and 0.02 for Binadhan 6 and 23.08% and 0.11 for TNDB 100 whereas Y 1281 cultivar was monomorphic indicating the existence of high level of intra cultivar genetic variation in Basmati 370 and TNDB, respectively 100. High levels of population differentiation (GST = 0.75) and low levels of gene flow (Nm = 0.16) estimates across all the loci indicate sufficient existence of genetic variation among these six cultivars. Low intra cultivar variation and significant differentiation in different cultivar pairs was observed at a number of loci. Nei’s genetic distances estimated among the different pairs of cultivars were correlated with geographical distances. The UPGMA dendrogram based on Nei’s genetic distance clubbed the cultivars into three clusters. RAPD analysis showed promise as an effective tool in estimating genetic polymorphism in different rice cultivars.