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We have analyzed SSRs in mitochondrial and chloroplast genomes of rice. We identified 2528 SSRs in the mitochondrial genome and average 870 SSRs in the chloroplast genomes. About 8.7% of the mitochondrial and 27.5% of the chloroplast SSRs were observed in the genic region. Dinucleotides were the most abundant repeats in genic and intergenic regions of the mitochondrial genome while mononucleotides were predominant in the chloroplast genomes. The rps and nad gene clusters of mitochondria had the maximum repeats, while the rpo and ndh gene clusters of chloroplast had the maximum repeats. We identified SSRs in both organellar genomes and validated in different cultivars and species.

With the objective of identifying SSR markers that can distinguish parental lines of rice hybrids, we characterized 10 each of cytoplasmic male sterile (CMS) and restorer (R) lines along with 10 popular Indian rice varieties using a set of 48 hyperpolymorphic SSRs distributed uniformly across the rice genome. All the SSR markers were polymorphic, amplifying a total of 163 alleles, with an average of 3.36 § 1.3 allelic variants per locus. Twenty-seven SSR markers showed ampliWcation of an allele, which was very speciWc and unique to a particular parental line and not ampliWed in any other rice genotype tested. Through multiplex PCR, SSR marker combinations that were unique to a particular parental line or hybrid were also identiWed. With a set of 10 SSR markers, all the public bred Indian rice hybrids along with their parental lines could be clearly distinguished. To utilize these SSR markers eVectively for detection of impurities in parental lines, a two dimensional bulked 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 CMS line IR58025A. We have also designed a multiplex PCR strategy involving single tube analysis using 2-3 markers for hybrid seed purity assessments and demonstrate its superiority over single marker analysis in accurate detection of impurities in hybrids. Implications of parental and hybrid speciWc SSR markers and strategies to utilize the informative SSR markers for detection of contaminants in a cost eVective manner are discussed.

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