rep-PCR helps to distinguish different alloplasmic cytoplasmic male sterile lines of Brassica juncea

Cytoplasmic male sterility (CMS) in higher plants is encoded by the mitochondrial genome. Several evidences support the view that organelle genomes of eukaryotes are derived from ancestral prokaryotic symbioants. Hence, it is expected that techniques suitable for distinguishing prokaryotes will be useful for distinguishing organelle genomes. Repetitive sequence based polymerase chain reaction (rep-PCR) technique is widely employed to identify different bacterial strains. We, therefore, tested the utility of rep-PCR for distinguishing different CMS lines of Brassica juncea. Using just three sets of rep-PCR primers, all the six Brassica lines could be unambiguously identified. Cloning and sequencing of a unique 1.5 kb amplicon obtained with Box1AR primer and template DNA of CMS catholica (W), indicated that the amplicon is indeed derived from mitochondrial genome. Further, based on sequence information of the 1.5 kb clone, a sequence characterized amplified region (SCAR) primer capable of distinguishing CMS catholica (W) from other lines was identified. The advantages of rep-PCR over other methods for distinguishing CMS lines are discussed.