Utilization of SSR Markers for Seed Purity Testing, In Popular Rice Hybrids (Oryza sativa L.)

Abstract

Microsatellite markers were used for fingerprinting of hybrids, assessing variation within parental lines and testing the genetic purity of hybrid seed lot in rice. In this study 35 simple sequence repeats (SSR) markers were employed for fingerprinting 2 popular rice hybrids and their parental lines. Six SSR markers were found polymorphic across the hybrids and produced unique fingerprint for the 2 hybrids. A set of five markers (RM 206, RM 276, RM 204, RM 234 and RM 228) differentiated the 2 hybrids from each other, which can be used as referral markers for unambiguous identification and protection of these hybrids. The analysis of plant-to-plant variation within the parental lines of the hybrid KRH-2 and DRRH-2, using informative markers indicated residual heterozygosity at two marker loci. This highlights the importance of SSR markers in maintaining the genetic purity of the parental lines. To utilize these SSR markers effectively for detection of impurities in hybrids, a two dimensional  DNA sampling strategy involving a 20 × 20 grow-out matrix has been designed and used for detection of contaminants in a seed-lot of the popular Hybrids viz., KRH-2 and DRRH-2. The validation of the identified markers was done with conventional grow out test (GOT) and they were comparable with the GOT.