Identification of informative EST-SSR markers capable of distinguishing popular Indian rice varieties and their utilization in seed genetic purity assessments

The present investigation was carried out with the following objectives: (i) to identify EST-SSR marker allele(s) capable of distinguishing 12 popular rice varieties cultivated in India, and (ii) to validate the utility of the genotype specific EST-SSR markers in seed genetic purity assessments. A set of 98 EST-SSR markers located across the 12 chromosomes of rice were used for finger-printing the selected rice varieties, out of which 24 EST-SSR markers were observed to be informative enough to distinguish all the 12 rice varieties considered in the study. A set of nine EST-SSR markers (RMES2-1, RMES2-2, RMES7-2, RMES12-2, JGT03-29.2, JGT07-22.8, JGT07-25.2, JGT10-5.7 and JGT12-18.6) exhibited unique alleles for seven rice varieties (Swarna. MTU 1001, Tellahamsa, Krishnahamsa, JGL 384, JGL 1798 and Vikas) and could serve as molecular IDs (Identities) for these varieties. To validate the utility of the EST-SSR markers in genetic purity assessment, foundation seed lots of MTU 1001, Tellahamsa, Krishnahamsa and Vikas were assessed for their genetic purity using both EST-SSR marker analysis and 12 morphological characters in a grow-out test (GOT). The impurities detected in the EST-SSR marker analysis were 2-3% higher as compared to those detected based on morphological characters in GOT. The results indicated practical utility of the EST-SSR markers in assessing the genetic purity of the rice varieties.