Abstract

The microsatellite or simple sequence repeat (SSR) markers were used to determine the allelic diversity and relationship among 48 traditional indigenous aromatic rice germplasm grown under Eastern part of India.  Out of 30 primers, 12 primers showed DNA amplification and polymorphism among 48 aromatic rice genotypes. A total of 28 bands appeared by using 12 SSR primers in 48 aromatic rice varieties/landraces. The number of alleles per locus ranged from 1 to 5 with an average 2.08. Out of 28 bands, 25 bands were polymorphic and three were monomorphic bands. The results reveal that all the tested primers showed distinct polymorphism among the landraces/varieties indicating the robust nature of SSR markers. Most of the primers showed highest polymorphic information content (PIC). Phenotypic characteristics are significantly correlated with genotypic characters. The cluster analysis indicates that the 48 traditional indigenous aromatic rice genotypes were grouped into two major clusters. Among the two major clusters, one cluster had 11 varieties and the second cluster had 37 varieties on the basis of the group of land races. Based on this study, the larger range of similarity values using SSR markers provides greater confidence for the assessment of genetic relationships among the varieties. The information obtained from the SSR profile helps to identify the variety diagnostic markers in 48 traditional indigenous aromatic rice genotypes. Significant genetic variation at maximum number of loci between varieties indicates rich genetic resources in rice. The intra and inter genetically variation might be useful for breeders to improve the aromatic rice varieties through selective breeding and cross breeding programs and also protect these unique germplasm under Intellectual Property Rights (IPR).

Key words: Aromatic Rice, Oryza sativa, DNA profile, diagnostic polymerase chain reaction simple sequence repeat (PCR-SSR) marker, polymorphism, genetic diversity.

Abbreviation

CBT, Conservation of biological diversity; CTAB, N-cetyl-N, N, N-trimethyl ammonium bromide; PCA, principal component analysis; SSRs, simple sequence repeats; PCR, polymerase chain reaction; PIC, polymorphic information content.