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Not AvailableThe realization of yield potential of rice (Oryza sativa L.) hybrids developed through the “three-line system” largely depends on genetic purity of parental lines. Cytoplasmic male sterile (CMS) lines often get contaminated with cognate isonuclear maintainer lines during multiplication. We report identification of a rice mitochondrial DNA sequence, possessing a repeat motif that is polymorphic between the wild abortive (WA)-CMS lines and their cognate isonuclear maintainer lines. We have designed a primer pair flanking the unique repeat and two fragments of different size were amplified in all WA-CMS and their maintainer lines through PCR. The PCR assay was able to precisely detect the impurities in a commercial seed lot of a popular CMS line, IR58025A. The possibility of utilizing this marker as a replacement for the morphology-based (grow-out test) GOT in accurate detection of contaminants in CMS seed stocks is discussed.Not Availabl