2008. Genome-wide analysis of the nitrogen stress transcriptome of red rice (Oryza sativa L.).

2008. Genome-wide analysis of the nitrogen stress transcriptome of red rice (Oryza sativa L.).

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ABTRACT

The weedy red rice (Oryza sativa L.) competes with cultivated rice (O. sativa) for N fertilizers, as demonstrated in field and greenhouse experiments. The ability of red rice to accumulate more N than cultivated rice even at low-N was hypothesized to be due to a molecular mechanism that helps it tolerate N deficiency stress better than the cultivated rice. Microarray analysis of the N stress transcriptome of the weedy red rice was conducted to identify expression patterns that could reveal signaling and response pathways in N deficiency stress adaptation. Candidate genes identified by microarray analysis were validated and their expression patterns in red rice were compared with those in Wells by semi-quantitative real-time RT-PCR. Microarray analysis revealed transcription factors and genes associated with signaling and response regulation, NH4+ assimilation, starch synthesis, stress response, protein fate, and energy metabolism. Gene expression profiles suggested that these genes compose an N deficiency stress response pathway that is likely underlying the greater tolerance of weedy red rice to N-limiting conditions compared to the cultivated rice. Real-time RT-PCR gene assays revealed that genes coding for two transcription factors as well as enzymes involved in starch synthesis, N assimilation, protein folding, and signaling and response regulation were differentially expressed in red rice and cultivated rice. Although these findings confirm the hypothesis that red rice has adaptive molecular mechanisms different from Wells rice, further experiments need to be done to investigate the specific processes involved in the response pathways regulated by these transcription factors and enzymes, particularly at time points immediately after N deficiency  .