Low temperature (LT) chilling damage often occurs at the seedling stage of rice growth, especially direct-seeded early indica rice, and flooding can alleviate the damage caused by LT chilling at the rice seedling stage. However, few studies have elucidated the molecular mechanism by which suitable flooding alleviates LT stress-induced damage. Therefore, LT, LT plus flooding (LTF) and control (CK) treatments were established at 8 degrees C for 3 days to determine the phenotype, agronomic traits and transcriptomic of direct-seeded early indica rice at the seedling stage. The results showed that compared with LTF, the seedling height, root number, fresh weight, dry weight and T3 (the 3rd leaf from the top) leaf length significantly decreased after LT treatment; LTF could reduce the damage of LT to the agronomic characters of rice seedlings. The physiological characteristics showed that compared with LT, LTF significantly decreased soluble protein content and CAT activity. Transcriptomic profiling showed that 5934 DEGs were identified from the rice leaves between the LT and CK comparison groups; 7658 DEGs were identified between the LTF and CK; and 2697 DEGs were identified between the LT and LTF treatment. In biological process, the 'metabolic process' was the most enriched subcategory. In cellular components, the three most enriched subcategories were 'cell', 'cell part' and 'organelle'. 'Binding' was the most enriched subcategory in molecular function. Differentially expressed genes (DEGs) were significantly enriched in photosynthesis, carotenoid biosynthesis, flavonoid biosynthesis, glycolysis gluconeogenesis, glycine, serine and threonine metabolism and plant hormone signal transduction pathways. Photosynthesis, energy metabolism and signal transduction pathway play important roles in flooding mitigation of LT stress. The results of this study may help to elucidate changes in physiological characteristics and gene expression through which flooding mitigates LT stress.
