Genetic Diversity Studies using SSR and EST-SSR Markers in Maintainer Lines of Rice Hybrids

Abstract

The performance and heterosis of hybrids are associated with genetic divergence between their parental lines. The present study has been conducted at ICAR-Indian Institute of Rice Research to assess the genetic diversity of 29 rice genotypes including rice hybrid maintainer lines using selected nine EST (Expressed Sequence Tag) based and thirteen reported SSR (Simple Sequence Repeats) markers to identify distinguishable alleles. All nine EST derived microsatellite markers were found to be polymorphic and generated total of 29 alleles in the 29 genotypes. The number of alleles per SSR marker ranged from 2-4 with an average value of 3.2. The polymorphic information content (PIC) for these SSR markers ranged from 0.68 (RMES 9-2) to 0.89 (RMES 5-2) and marker RMES 3-2, RMES 5-2, RMES 6-1, RMES 9-2 generated maximum four alleles. For reported SSR markers, the number of alleles per marker ranged from 1-3 with an average value of 1.9. The PIC value ranged from 0.59 (RM25645) to 0.89 (RM10290) and markers RM25640, RM25645, RM25672, RM10300, RM25641 generated maximum three alleles. This study highlights that EST derived SSR markers are efficient and suitable for assessing the genetic relatedness of the genotypes and studied maintainer lines exhibited high level of genetic diversity