• Glycine betaine (GB), a quaternary ammonium solute, plays a crucial role in developing osmotic tolerance. Rice contains a choline monooxygenase ( CMO) and two betaine aldehyde dehydrogenase homologues that are required for GB synthesis, but usually no GB is accumulated in rice ( Oryza sativa). • To elucidate the molecular processes that underlie the GB deficiency in rice, an experiment involving rice and spinach ( Spinacia oleracea) was conducted to analyze the products transcribed from CMO genes. Reverse transcription-polymerase chain reaction (RT-PCR) was used to obtain CMO transcripts and a sequencing approach was employed to analyze the structural composition of various CMO transcripts. • The results showed that most rice CMO transcripts were processed incorrectly, retaining introns or deleted of coding sequences; the unusual deletion events occurred at sequence elements of the short-direct repeats. • In conclusion, the production of incorrect CMO transcripts results in a deficiency of the full-length CMO protein and probably reduces GB accumulation considerably in rice plants. Sequence comparison results also implied that the unusual deletion-site selection might be mediated by the short-direct repeats in response to stress conditions. [ABSTRACT FROM AUTHOR]