Two specific fragments OPJ18-1000 and OPJ18-1400 were obtained from mitochondrial DNAs of two rice varieties, II-32 and II you 949, by RAPD analysis. The sequenced lengths of the two differential fragments were 1068 bp and 1481 bp, respectively. The result of Southern hybridization demonstrated that the differential fragments were true. When hybridizing with II-32A, II-32B and II you 949 by OPJ18-1000 probe, we found OPJ18-1000 which had effects on rice II-32A and II you 949 cytoplasmic male sterility in transcription had not the same effects on II-32B. Though RNA dot hybridization was negative, OPJ18-1400 had a conservative domain of seven base pairs DNA sequence: 5'-TTCCCTC-3', which was homologous recombination hotspot domain in atp6 gene. It was reported that 5'-TTCCCTC-3' induced the formation of chimeric gene in mitochondrial DNA and further caused rice male sterility. As a result, the two fragments are new mitochondrial DNA fragments relevant to rice cytoplasm male sterility by homologous analysis and DNA, RNA hybridization.
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