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.

Botanical compounds with herbicidal activity exhibit safety, low toxicity, and low chances of herbicide resistance development in plants. They have widespread applications in green agricultural production and the development of organic agriculture. In the present study, dihydrocoumarin showed potential as a botanical herbicide, and its phenotypic characteristics and mechanism of action were studied in barnyardgrass [Echinochloa crus-galli (L.) P.Beauv.] seedlings. The results indicated that dihydrocoumarin inhibited the growth of barnyardgrass without causing significant inhibition of rice seedling growth at concentrations ranging between 0.5 and 1.0 g/L. Additionally, dihydrocoumarin treatment could cause oxidative stress in barnyardgrass, disrupt the cell membrane, and reduce the root cell activity, resulting in root cell death. Transcriptomic analyses revealed that dihydrocoumarin could inhibit barnyardgrass normal growth by affecting the signal transduction of plant hormones. The results showed significant differential expression of plant hormone signal transduction genes in barnyardgrass. Additionally, dihydrocoumarin interfered with the expression of numerous phenylpropanoid biosynthesis genes in barnyardgrass that affect the production of various vital metabolites. We speculate that the barnyardgrass growth was suppressed by the interaction among hormones and phenylpropanoid biosynthesis genes, indicating that dihydrocoumarin can be applied as a bioherbicide to control barnyardgrass growth in rice transplanting fields.

Submergence stress is a major constraint in direct-seeded rice production. This study investigated the effect and biochemical mechanism of sprouting, a traditional agronomic practice, on improving submergence tolerance in rice. Our findings demonstrate that sprouting is an effective seed treatment that significantly enhances the plant’s ability to withstand flooding. Specifically, 48 h sprouting increased shoot height and root length by 163% and 423%, respectively, in the YLYJ48 variety under 6-day submergence. Sprouting upregulated the activity of glutathione reductase (GR) and the expression of its related genes, thereby significantly promoting the biosynthesis of glutathione (GSH). GSH content in seeds increased from 64.86 µg g⁻¹ FW (0 h) to 83.00 µg g⁻¹ FW (48 h) in HZ, and from 82.14 to 92.52 µg g⁻¹ FW in YLYJ48. This process provides critical antioxidant protection for seedlings to implement a rapid “escape strategy,” ultimately enhancing their submergence tolerance. Functional verification showed that seed soaking with exogenous GSH (0.1%) effectively improved submergence tolerance by increasing antioxidant reserves. Exogenous GSH treatment elevated shoot height by approximately 50% in both HZ and YLYJ48 varieties under submergence. Field trials further demonstrated that exogenous GSH application significantly enhanced seedling establishment rates by 30–35% and improved seedling growth traits under submergence tolerance stress across multiple rice varieties. This study reveals part of the mechanism by which sprouting enhances submergence tolerance by influencing glutathione metabolism, offering practical strategies for flood-resilient direct-seeded rice cultivation.

Barnyardgrass (Echinochloa crus-galli L.) is the most serious weed threatening rice production, and its effects are aggravated by resistance to the quinclorac herbicide in the Chinese rice fields. This study conducted a comparative proteomic characterization of the quinclorac-treated and non-treated resistant and susceptible E. crus-galli using isobaric tags for relative and absolute quantification (iTRAQ). The results indicated that the quinclorac-resistant E. crus-galli had weaker photosynthesis and a weaker capacity to mitigate abiotic stress, which suggested its lower environmental adaptability. Quinclorac treatment significantly increased the number and expression of the photosynthesis-related proteins in the resistant E. crus-galli and elevated its photosynthetic parameters, indicating a higher photosynthetic rate compared to those of the susceptible E. crus-galli. The improved adaptability of the resistant E. crus-galli to quinclorac stress could be attributed to the observed up-regulated expression of eight herbicide resistance-related proteins and the down-regulation of two proteins associated with abscisic acid biosynthesis. In addition, high photosynthetic parameters and low glutathione thiotransferase (GST) activity were observed in the quinclorac-resistant E. crus-galli compared with the susceptible biotype, which was consistent with the proteomic sequencing results. Overall, this study demonstrated that the resistant E. crus-galli enhanced its adaptability to quinclorac by improving the photosynthetic efficiency and GST activity.

S-metolachlor is a selective pre-emergence herbicide used in dryland. However, it is challenging to employ in paddy fields due to its phytotoxic effects on rice. As a common phytohormone, Gibberellin-3 (GA₃) is inferred to have the ability to alleviate herbicide phytotoxicity. This study first quantitatively verified the phytotoxicity of s-metolachlor to rice and then demonstrated the mitigative effect of GA₃ on these adverse reactions. Furthermore, a transcriptome of rice seedlings subjected to different treatments was constructed to assemble the reference genes, followed by comparative metabolomics and proteomics analyses. Metabolomics revealed an enrichment of flavonoid metabolites in the group of adding GA₃, and these flavonoids can eliminate ROS in plants. Proteomics analysis indicated that differential proteins were enriched in the phenylpropanoid biosynthesis pathway responsible for the synthesis of flavonoids and that the functions of most differential proteins are associated with peroxidase. The proteome, combined with the transcriptome, revealed that the expressions of proteins and genes was related to the POD activity in the group of adding GA₃. It was speculated that the elimination of ROS is key to alleviating the stress of s-metolachlor on rice growth. It was inferred that the mechanism of GA₃ in alleviating the phytotoxicity of the substance s-metolachlor is by increasing the activity of the POD and influencing the growth of rice seedlings through the restoration of flavonoid synthesis. In this study, we screened GA₃ as a safener to alleviate the phytotoxicity of s-metolachlor on rice. On this basis, the mechanism of alleviating phytotoxicity was studied. The application range of s-metolachlor might be expanded, providing a new supplementary method for weed control and herbicide resistance management.

Echinochloa crus−galli is one of the world’s ten most pernicious weeds and is mainly controlled by chemical herbicides. However, the application of herbicides over long periods has escalated weed resistance, highlighting the need for eco−friendly alternatives. As a degradable natural allelochemical, dihydrocoumarin displays auxin−like activity and inhibits root growth in E. crus−galli in a manner dependent on concentration, phenotypically mimicking exogenous IAA. Previous studies have shown that dihydrocoumarin suppresses weed growth largely via auxin signaling. Here, we identified EcIAA9, a gene that responds to dihydrocoumarin and encodes a nuclear protein interacting with EcARF7. Heterologous rice assays showed that at 25 mg/L dihydrocoumarin, EcIAA9 overexpression increased primary−root inhibition from 30.81% (WT) to 54.44% and 52.00% (EcIAA9−OE). Conversely, OsIAA9 knockout lines consistently exhibited a milder root inhibition trend compared to the overexpression lines. These differential phenotypes collectively establish IAA9 as a key positive regulator in this pathway. Notably, EcIAA9 overexpression rice showed different responses to dihydrocoumarin and IAA, and combined treatments produced additive inhibitory effects. Knockout of OsARF7 failed to fully abolish dihydrocoumarin−triggered inhibition, indicating that ARF7 participates in this regulatory module, although functional compensation among ARF homologs may underlie this observation. In summary, the EcIAA9–EcARF7 regulatory module contributes to the repression of root growth triggered by dihydrocoumarin. These findings show that dihydrocoumarin phenotypically mimicked the inhibitory effect of IAA on barnyardgrass but acted through a somewhat different mechanism. This study provides new insights into the crosstalk between allelochemicals and auxin signaling.