The invention relates to a method of using DNA sequences for assessing seed purity. More specifically, the invention relates to a DNA sequences having homology to rice mitochondrial DNA and being unique to Wild Abortive (WA) cytoplasm containing cytoplasmic male sterile lines of rice, and the use of these sequences in a Polymerase Chain Reaction (PCR) assay to distinguish Male Sterile (CMS) lines of rice from their cognate Male Fertile Maintainer Lines.