Rice (Oryza sativa L.) is one of the most significant food crops worldwide. Flooding can significantly impact the survival and emergence of rice seedlings in the direct planting form of rice, leading to a loss of production. This work investigated the critical phase of rice seed germination to the seedling establishment under submergence stress. It also explored the underlying physiological and molecular processes of shoot and root submergence tolerance. Physiological and transcriptomic analysis of flood-tolerant varieties (LS273) and non-flood-tolerant varieties (ZZ39) were performed. Under submergence stress, LS273 showed longer roots, taller shoots than ZZ39, and lower levels of malondialdehyde and GSSG, but a greater level of GSH/GSSG. In response to stress induced by submersion, LS273 produces more auxin than ZZ39. Within shoots, 4285 DEGs specific to LS273 and 4389 DEGs specifics to ZZ39 were found using the RNA-seq technique. There were 3983 specific DEGs in LS273 and 3292 specific DEGs in ZZ39 in the roots. Antioxidants and plant growth hormones were primarily mentioned in the annotations for these DEGs. Overall, our research provides a thorough foundation for investigating the molecular network underlying shoots’ and roots’ resistance to submergence stress in rice seedlings, leading us to hypothesize that the resistance of flood-tolerant rice may be attributed to high levels of oxidation resistance and auxin accumulation.

Rice (Oryza sativa L.) is one of the most important food crops worldwide. However, during direct seeding, rice is extremely vulnerable to flooding stress, which impairs rice’s emergence and seedling growth and results in a significant yield loss. According to our research, chitosan oligosaccharides have the potential to be a chemical seed-soaking agent that greatly increases rice’s resistance to flooding. Chitosan oligosaccharides were able to enhance seed energy supply, osmoregulation, and antioxidant capacity, according to physiological index assessments. Using transcriptome and metabolomic analysis, we discovered that important differential metabolites and genes were involved in the signaling pathway for hormone synthesis and antioxidant capacity. Exogenous chitosan oligosaccharides specifically and significantly inhibit genes linked to auxin, jasmonic acid, and abscisic acid. This suggested that applying chitosan oligosaccharides could stabilize seedling growth and development by controlling associated hormones and reducing flooding stress by enhancing membrane stability and antioxidant capacity. Finally, we verified the effectiveness of exogenous chitosan oligosaccharides imbibed in seeds by field validation, demonstrating that they can enhance rice seedling emergence and growth under flooding stress.