Transcriptome Analysis Reveals Quality Improvement Mechanisms in Ratoon Rice

Ratoon rice offered higher yields and superior grain quality compared to main rice. This study compared differences in germination, chalkiness, and antioxidant enzyme activities between ratoon rice and main rice of cultivars 19X and NJXM, and analyzed the underlying quality improvement mechanisms from a transcriptome perspective. The results demonstrated that ratoon rice exhibited a significantly greater germination potential and germination rate, reduced chalky grain rate and chalkiness degree, and exhibited higher activities of superoxide dismutase (SOD) and catalase (CAT). Transcriptome analysis revealed that the enhanced germination in ratoon rice may result from significantly upregulated expression of genes qLTG3-1, OsLOX2, OsSAMDC2, and OsSAMDC4. The reduction in chalkiness in ratoon rice may involve the following three causes. First, the reduction of chalkiness may be due to the significantly upregulated GAD3 expression by enhancing high-temperature tolerance. Second, the significantly upregulated expression of peroxidase genes (prx86, POX8.1, Perox4) and significantly downregulated OsEBP89 expression potentially increased the oxidative stress tolerance to reduce the chalkiness of ratoon rice. Finally, the significantly upregulated OsNCED3 expression potentially modulated plant hormones to decrease the chalkiness of ratoon rice. These findings provided novel insights into revealing the mechanisms underlying the superior quality of ratoon rice.