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.

The Clearfield^® technology is an useful tool for controlling weedy rice due to the effectiveness of imazamox and the cultivation of rice varieties resistant to imidazolines. However, residual imazamox in the soil probably causes phytotoxicity to subsequent non-resistant rice crops. We previously found that pyrroloquinoline quinone (PQQ), a bioactive elicitor, can enhance rice tolerance to imazamox. In this study, we explored the molecular mechanism of PQQ-mediated rice tolerance to imazamox by RNA-seq analysis, real-time quantitative PCR (RT-qPCR) assay, and enzyme activity assay. The results indicated that compared to imazamox at 66.7 mg a.i./L (IMA) alone, rice plants treated with imazamox at 66.7 mg a.i./L and PQQ at 0.66 mg a.i./L (IMA + PQQ) exhibited significantly reduced sensitivity to imazamox. Seven days post-treatment, IMA + PQQ-treated rice plants showed partial chlorosis and leaf curling, but IMA-treated rice plants had severe wilting and died. The fresh weight inhibition rate was 29.3% in the IMA + PQQ group, significantly lower than that of 56.6% in the IMA group alone. RNA-seq analysis showed differentially expressed genes were mainly involved in phenylpropanoid biosynthesis, diterpenoid biosynthesis, and MAPK signaling pathways in response to IMA + PQQ treatment. Both RNA-seq analysis and RT-qPCR assay showed that the expression of OsCATB gene in the catalase (CAT) gene family was upregulated at 12 h, the expression of OsGSTU1 gene was upregulated at 12, 24, and 48 h, while the expressions of OsABCB2, OsABCB11, and OsABCG11 genes were upregulated at 24 and 48 h. Enzyme activity assays revealed that the activity of superoxide dismutase in the IMA + PQQ group was increased by 47.45~120.31% during 12~72 h, compared to that in the IMA group. CAT activity in the IMA + PQQ group was increased by 123.72 and 59.04% at 12 and 48 h, respectively. Moreover, malondialdehyde levels indicative of oxidative damage were consistently lower in IMA + PQQ-treated plants, with a reduction of 46.29, 11.37, and 14.50% at 12, 36, and 72 h, respectively. Overall, these findings discover that PQQ has potential in reducing imazamox phytotoxicity in rice by enhancing antioxidant enzyme activities and regulating oxidative stress responses. They will provide valuable strategies for improving imazamox tolerance in crops.

Using bioactive inducers to enhance rice resistance is an effective means of green prevention and control of diseases during rice production. In a previous study, we found that foliar sprays of pyrroloquinoline quinone (PQQ) as the bioactive inducer could remarkably reduce the occurrence index of rice sheath blight (ShB) Rhizoctonia solani and increase the grain yield of rice under field conditions. However, little information is available on the mechanism of PQQ-induced rice resistance to ShB. In this study, the phenotype and mechanism of foliar sprayed PQQ-induced rice resistance to ShB were investigated by artificial inoculation method, RNA-seq technology, and quantitative real-time PCR (qRT-PCR) assay in the laboratory. The results showed that at 144 h after inoculation (hai) with the ShB C30 strain, many disease spots occurred obviously in a susceptible variety, Lemont (L), treated by 1.0 μmol/L PQQ (P+) with the disease score (DS) of 4.36, and almost all plants were withered and died under the ddH₂O (P−) treatment alone, with the DS of 8.39. By comparison, the DS of a resistant variety, Gaopin 6 (G), was only 0.88 in the P+ treatment and 3.82 in the P− treatment. The results of hormone determination showed that jasmonic acid (JA) contents in the G and L varieties treated by P+ were increased significantly, by 78% and 197% respectively, at 48 hai. There was no significant difference in salicylic acid (SA) contents in these varieties between P+ and ddH₂O (P−) treatments during the period of 48 hai. These results suggest that JA may play a key role in PQQ-induced rice resistance to ShB. The transcriptome analysis of the leaf sheath of the G and L varieties indicated that 165 and 250 differentially expressed genes (DEGs) were found in the intersection of LP− vs. LP+ and GP− vs. GP+ at 24 and 48 hai, respectively. Kyoto encyclopedia of genes and genomes analysis showed that these DEGs were related to plant–pathogen interaction, ribosome, plant hormone signaling transduction, mitogen-activated protein kinas signaling pathway, and phenylpropanoid biosynthesis. For ten highly expressed genes related to disease resistance, the results of qRT-PCR assay showed that eight genes, especially OsAOS2 and OsOSM1, were regulated positively, and two genes, OsGF14e and OsWRKY72, were regulated negatively. Among these, four up-regulated genes, OsOSM1, OsAOS2, OsHI-LOX, and OsLOX1, and one down-regulated gene, OsWRKY72, belonging to the JA signaling pathway, may be involved in PQQ-induced rice resistance to ShB. These results provide valuable information for green prevention and control of ShB by PQQ foliar spraying in the field.

Mutagenesis breeding, combined with the application of corresponding herbicides to develop herbicide-resistant rice germplasm, provides great promise for the management of weeds and weedy rice. In this study, a topramezone-resistant rice mutant, TZR1, was developed from the indica rice line Chuangyu 9H (CY9H) through radiation mutagenesis and topramezone selection. Dose–response curves revealed that the resistance index of TZR1 to topramezone was 1.94-fold compared to that of CY9H. The resistance mechanism of TZR1 was not due to target-site resistance. This resistance could be reversed by a specific inhibitor of glutathione S-transferase (GST). The activity of antioxidant enzymes was analyzed. SNPs and Indels were detected using whole-genome resequencing; differentially expressed genes were identified through RNA sequencing. Then, they underwent Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. Key candidate genes associated with topramezone resistance were validated via a real-time quantitative PCR assay. Five GST genes, two UDP-glycosyltransferase genes, and three ATP-binding cassette transporter genes were identified as potential contributors to topramezone detoxification in TZR1. Overall, these findings suggest that GST enzymes possibly play an important role in TZR1 resistance to topramezone. This study will provide valuable information for the scientific application of 4-hydroxyphenylpyruvate dioxygenase inhibitors in paddy fields in future.

This study has investigated the occurrence characteristics and population damage of weeds in double-cropping direct-seeded rice fields in Hunan, and has identified efficient and safe pre- and post-emergence herbicides to enhance resistance management. Field trials were conducted at two representative sites (Yiyang and Changsha) in Hunan in 2024~2025. Weed community composition and emergence patterns were systematically monitored. The inhibitory effects of weed infestations on rice growth and yield were quantified. The biological activity and field efficacy of various herbicide classes against barnyardgrass (Echinochloa crus-galli) were evaluated via greenhouse bioassays and field trials. Weed emergence lasted 3–48 days after sowing (DAS) with three distinct peaks. Grasses emerged earliest and dominated the community, with barnyardgrass peaking at 13–17 DAS (≈50% of total weeds), followed by broadleaves at 20 DAS (≈40%) and sedges at 25 DAS (96.8% control at 20 and 40 days after treatment (DAT), while oxaziclomefone (66 g ai ha⁻¹) achieved 88.2% control at 20 DAT. For post-emergence herbicides, Profoxydim showed the highest intrinsic activity (GR₉₀ = 33.01 g ai ha⁻¹), followed by feproxydim (GR₉₀ = 33.45 g ai ha⁻¹) and flusulfinam (GR₉₀ = 64.55 g ai ha⁻¹). In field trials, flusulfinam provided 100% control with superior crop safety at 20 and 40 DAT, while Florpyrauxifen-benzyl, feproxydim, and metamifop reached >93% efficacy. In conclusion, weed emergence in Hunan direct-seeded rice follows a three-peak pattern, with barnyardgrass being the most destructive species. An integrated strategy combining pretilachlor (pre-emergence) and flusulfinam (post-emergence), rotated with florpyrauxifen-benzyl and feproxydim, is recommended for effective barnyardgrass management and resistance mitigation.