Identification of genotype specific alleles and molecular diversity assessment of popular rice (Oryza sativa L.) varieties of India.

Abstract

The study was done with an aim to develop molecular tags for rice lines. A set of 29 accessions of Indian popular rice varieties was subjected to diversity study using simple sequence repeat (SSRs), a total of 87 alleles were produced that were 100% polymorphic. Twelve sets of SSR primers amplified specific alleles in 14 genotypes. The PIC value ranged from 0.57 (RM 313) to 0.98 (RM 442 and RM 163) with average of 0.78 and average genetic similarity of 0.38 was observed among the popular varieties. The maximum similarity of 0.82 was observed between Jayshree and Sarjoo52 and minimum similarity of 0.05, between Jaya and Pusa Basmati 1. Based on ecologies and duration groups showed a maximum similarity of 0.34 between IRM and RSL groups and a minimum similarity of 0.18 between IRE and RSL groups. Cluster analysis revealed PCA of rice microsatellite data from 20 primer pairs separated the four early varieties and land races from recently evolved varieties by the first and second principal component, which represent 15 and 12.2% of diversity in the sample. Out of 29 genotype, 14 genotypes produced specific alleles, which can be used as molecular tags for particular genotypes when utilized along with the non polymorphic markers in this set of genotypes it produces bar-coded molecular tags for the identification of the valuable new plant lines.