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Background  The application of hybrid rice technology has significantly increased global rice production during the last three decades. Approximately 90% of the commercially cultivated rice hybrids have been derived through three-line breeding involving the use of WA-CMS lines. It is believed that during the 21 st  century, hybrid rice technology will make significant contributions to ensure global food security. This study examined the poorly understood molecular basis of the WA-CMS system in rice.    Results  RFLPs were detected for  atp6  and  orfB  genes in sterile and fertile rice lines, with one copy of each in the mt-genome. The RNA profile was identical in both lines for  atp6 , but an additional longer  orfB  transcript was identified in sterile lines. 5' RACE analysis of the long  orfB  transcript revealed it was 370 bp longer than the normal transcript, with no indication it was chimeric when compared to the genomic DNA sequence. cDNA clones of the longer  orfB  transcript in sterile lines were sequenced and the transcript was determined unedited. Sterile lines were crossed with the restorer and maintainer lines, and fertile and sterile F 1  hybrids were respectively generated. Both hybrids contained two types of  orfB  transcripts. However, the long transcript underwent editing in the fertile F 1  hybrids and remained unedited in the sterile lines. Additionally, the editing of the 1.1 kb  orfB  transcript co-segregated with fertility restoring alleles in a segregating population of F 2  progeny; and the presence of unedited long  orfB  transcripts was detected in the sterile plants from the F 2  segregating population.    Conclusion  This study helped to assign plausible operative factors responsible for male-sterility in the WA cytoplasm of rice. A new point of departure to dissect the mechanisms governing the CMS-WA system in rice has been identified, which can be applied to further harness the opportunities afforded by hybrid vigor in rice.

An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of Oryza sativa L. subsp. indica