The phyB mutant exhibits robust salt tolerance via enhanced K⁺/Na⁺ homeostasis, proline accumulation, and membrane stability. Transcriptomics reveals PHYB coordinates a unique early-response network involving transcription factors, kinesins, and DNA metabolism. Integrated population eQTL analysis and transcriptional regulation prediction condense a core salt-tolerance module of four transcription factors, three kinesins, and six DNA metabolism genes. This study identifies actionable targets for genetic improvement of salt-tolerant varieties. Soil salinization poses a significant threat to global rice production, underscoring the urgent need to improve salt tolerance as a key strategy for ensuring food security. In this study, we report that the phytochrome B (phyB) mutant exhibits robust salt tolerance via enhanced K⁺/Na⁺ homeostasis, proline accumulation, and membrane stability. Transcriptomic profiling revealed that phyB modulates salt adaptation via transcription factor activity, DNA metabolism, and motor activity. Utilizing the salt-responsive expression quantitative trait loci (eQTL) data from global mini-core rice collection comprising 202 accessions, we systematically screened enriched Gene Ontology (GO) terms and predicted a set of core salt tolerance-related genes at genomic level in the phyB mutant. Transcriptional regulation analysis established a regulatory network in which four transcription factors potentially regulate three kinesin genes and six DNA metabolism-related genes. Luciferase (LUC) assays further confirmed that these transcription factors directly activate the promoters of downstream genes. Heterologous expression in yeast demonstrated that a representative transcription factor (Os10g0371100), a kinesin (Os05g0397900), and a DNA metabolism-related gene (Os01g0944900) significantly promoted yeast growth under salt stress conditions, indicating conserved functions. Collectively, these findings elucidate a novel molecular network through which PHYB deficiency enhances salt tolerance by integrating transcription factor activity, DNA metabolism, and motor activity, and provide a set of core candidate genes for the genetic improvement of salt tolerance in rice.

Low temperature severely impairs rice growth and productivity. Although the OsEIN2-OsEIL1/2 signaling pathway has been reported to negatively regulate chilling tolerance via OsICE1 in rice, the full regulatory network remains unclear. Here, we demonstrate that OsEIL1/2 negatively regulates chilling tolerance by promoting OsMYB30 expression and enhancing reactive oxygen species (ROS) accumulation. RT-qPCR, yeast one-hybrid assay, EMSA and ChIP-qPCR assay revealed that OsEIL1/2 directly target the promoter of OsMYB30 and activate its expression. Furthermore, we found that OsMYB30 modulates ROS homeostasis by regulating ascorbate peroxidase (OsAPX3) and peroxidase (OsPRX12//41/136) expression under chilling stress. Importantly, association analysis revealed a superior haplotype of OsMYB30 (Hap1), prevalent in japonica rice, which is linked to enhanced seedling survival under chilling stress. Taken together, our findings elucidate a novel mechanism of OsEIN2-OsEIL1/2 signal negatively regulates rice chilling tolerance through OsMYB30-mediated ROS homeostasis, Moreover, this study highlights the potential of Hap1 for breeding chilling-tolerant rice varieties.

Salt-induced inhibition of tillering constrains rice plant architecture and yield potential. To clarify the molecular links between salt tolerance and tiller development, we compared physiological responses and tiller-bud transcriptomes of the salt-tolerant japonica cultivar Nipponbare (NIP) and the salt-susceptible cultivar Kongyu 131 (KY131) under salt stress. Time-resolved RNA sequencing revealed cultivar-specific transcriptional dynamics, suggesting that rapid acclimation and transcriptome stabilisation in tiller buds contribute to salt tolerance. Functional enrichment highlighted redox regulation, phenylpropanoid metabolism, chlorophyll biosynthesis, nitrogen metabolism, and phytohormone signalling as key processes coordinating salt adaptation and tiller-bud development. Co-expression analysis identified the NAC transcription factor OsNAC4 as a central regulatory hub. Functional analyses showed that OsNAC4 negatively regulates rice salt tolerance and tillering. Loss-of-function Osnac4 mutants exhibited enhanced salt tolerance, reduced ROS accumulation and membrane damage, increased antioxidant enzyme activities, and higher tiller number. Further analysis indicated that OsNAC4 functions as a transcriptional activator of stress-, redox-, metabolic-, and ABA-associated pathways, with OsNCED5 implicated as a downstream target mediating salt-induced ABA accumulation. Through integrated transcriptomic, physiological, and genetic evidence from comparative analyses, this study establishes a molecular connection between salt adaptation and rice tiller development and identifies candidate targets for breeding salt-tolerant rice with improved architecture.

Plant activators enhance disease resistance by priming host immunity, offering a sustainable alternative or complement to conventional pesticides. To advance this field, we established a high-throughput screening platform based on activation of the rice WRKY45 promoter, a central regulator of disease resistance. From a library of 80,232 compounds, we identified five novel plant immune-priming compounds (PIPC1–5) that significantly enhanced resistance to rice blast caused by Magnaporthe oryzae following seed or foliar application. These PIPCs showed no direct antifungal activity, indicating that they act through activation of host defense responses. The PIPCs also conferred broad-spectrum resistance to rice bacterial blight (Xanthomonas oryzae pv. oryzae), rice false smut (Ustilaginoidea virens), pepper spotted wilt (tomato spotted wilt virus), and downy mildew of Chinese cabbage (Hyaloperonospora brassicae). Notably, PIPCs lack the thiazole ring characteristic of classical salicylic acid (SA) pathway activators such as probenazole and benzothiadiazole, representing a novel chemical scaffold. Mechanistically, the PIPCs primed rice seedlings to establish immune memory by acting either upstream or downstream of SA synthesis, thereby accelerating defense gene induction upon subsequent pathogen challenge. These findings expand the repertoire of immune-priming agents for managing diverse and evolving crop pathogens.

Soil salinity critically impairs global rice productivity, necessitating the exploration of salt-tolerant genetic resources in wild rice (Oryza rufipogon). Here, we identified a C2H2 transcription factor, ST5, from wild rice using a chromosome segment substitution line population. Functional analysis reveals that ST5 negatively regulates rice salt tolerance. A 36-bp insertion in the ST5W promoter harbors two W-box motifs, transcription factor OsWRKY80 binds to this insertion and represses ST5W expression. This repression reduces ST5W expression, alleviating its negative regulation on the downstream genes OsCPK4, which are pivotal for maintaining Na+/K+ homeostasis under salinity stress. Notably, the ST5W allele is exclusively present in a few of O. rufipogon accessions and absent in all cultivated rice varieties. Field trials demonstrate ST5W significantly improves grain yield across diverse genetic backgrounds under saline field conditions. Our work provides both an underexploited genetic resource and molecular insights for breeding salt-tolerant rice varieties to address soil salinization challenges.

Saline-alkaline stress severely constrains rice productivity, posing a critical threat to global food security. Identifying uncharacterized salt-tolerance genes with agronomic value is therefore essential for breeding stress-resilient and high-yield rice varieties. In this study, we identify a previously unidentified gene, LOC_Os05g07260, by combining genome-wide association study and expression quantitative trait locus mapping, and designated it as Salt Tolerance Gene 5.2 (STG5.2), which encodes a phosphatidylinositol glycan-related protein. Functional validation reveals that STG5.2 acts as a positive regulator of both salt stress tolerance and yield-related traits in rice. STG5.2 may reprogram metabolic pathways and regulate the expression of salt-responsive genes including Na+ exclusion-related Salt Overly Sensitive 1 (OsSOS1), High-Affinity K+Transporter 2;1 (OsHKT2;1), and stress tolerance-positive regulator Acireductone Dioxygenase 1 (OsARD1), forming a multi-layered regulatory network for salt adaptation. Combined with phenotypic data from chromosome segment substitution lines, the superior STG5.2 haplotype, predominantly present in indica rice, shows great potential for improving salt tolerance in japonica backgrounds. Overall, our results highlight that STG5.2 may modulate rice salinity resilience by regulating ion homeostasis and the coordination of multiple stress-responsive pathways, providing a potential molecular basis for salt-tolerant rice varieties breeding.

Induced resistance primes host immunity for enhanced protection; however, how pathogens respond to this primed state remains poorly understood. Here, we investigated the molecular responses of the rice blast fungus Magnaporthe oryzae during infection of benzothiadiazole (BTH)-primed rice. Seed priming with BTH conferred long-lasting resistance against M. oryzae at the four-leaf stage. Time-course transcriptomic analyses (12-48 hpi) identified 699 differentially expressed genes (DEGs) in M. oryzae, revealing a distinct temporal transition during infection of BTH-primed rice. The fungal transcriptional response shifted from early growth and environmental sensing to enhanced protein turnover, metabolic repression, energy depletion, and genomic instability, indicating progressive impairment of fungal fitness by host immunity. From these DEGs, eight BTH-suppressed candidate virulence genes (MoBVG1-8) were selected for functional characterization. Gene overexpression analyses showed that two genes, MoBVG2 and MoBVG6, significantly increased pathogenicity on BTH-primed rice, while knockout analyses confirmed that both are required for full pathogenicity on non-primed control plants. MoBVG2 encodes a reactive oxygen species (ROS)-scavenging effector, and MoBVG6 encodes an environmental sensor, highlighting the importance of ROS detoxification and environmental perception for successful host colonization. Functional analyses further revealed that MoBVG2 contribute to vegetative growth, while MoBVG6 is required for proper appressorium development. Together, these findings suggest that BTH-induced resistance restricts blast disease by impairing fungal metabolic fitness and suppressing key virulence genes, providing novel insights into the pathogen-side molecular mechanisms underlying chemically induced resistance in plants.

Inconsistent nitrogen application rates across global croplands necessitate the adaptation of different genetic alleles to optimize nitrogen-use efficiency (NUE) in agriculture. In rice (Oryza sativa L.), different TEOSINTE BRANCHED 1, CYCLOIDEA AND PROLIFERATING CELL FACTOR 19 (OsTCP19) alleles contribute to the geographical adaptation to soil fertility. The nitrogen-sensitive allele OsTCP19-H is predominantly found in low-nitrogen regions due to its superior tillering and yield accumulation capabilities. Conversely, the nitrogen-insensitive allele OsTCP19-L is more common in nitrogen-sufficient regions, though the precise factors affecting this distribution remain unknown. Here, we report that high-nitrogen levels lead to lodging in an OsTCP19-dependent manner. Overexpression of this gene modifies plant architecture, enhancing lodging resistance in rice. Importantly, fine-tuning OsTCP19 expression can confer lodging resistance without a yield penalty. This is particularly important as it alleviates yield loss from lodging under high-nitrogen conditions and, intriguingly, can result in a substantial increase in plot yield when combined with dense planting strategies. Furthermore, the distinct nitrogen sensitivity of different OsTCP19 alleles allows for substantial improvement in grain yield and NUE under certain nitrogen conditions. Thus, our findings suggest that genetic manipulation of a single gene, OsTCP19, could allow flexible adaptation to diverse planting scenarios, maximizing genetic benefits based on local nitrogen availability.

The increasing challenge of managing crop diseases requires innovative and sustainable approaches. The current reliance on synthetic pesticides raises environmental concerns and contributes to the development of pesticide resistance. Therefore, exploration of alternative, eco-friendly biocontrol agents is crucial. In this article, we examine the underutilized potential of medicinal plant wastes (MPWs) as renewable and eco-friendly resources for the control of crop diseases. MPWs contain a significant portion of bioactive compounds with biopesticidal potential and represent a readily available and cost-effective source. Here, we review the recent findings on the efficacy of MPW extracts, discuss their mechanisms of action, and highlight their applications in crop protection. The contents presented herein emphasize the importance of MPW extracts as sustainable alternatives or complements to conventional synthetic pesticides and offer new possibilities for environmentally conscious strategies in crop disease management.

Soil alkalinization is a major environmental stress that severely limits plant growth and development. Rice (Oryza sativa) is a globally important food crop, and to improve its yield and quality in saline-alkaline environments, its molecular responses to alkaline stress must be better understood. Here, we cloned and overexpressed the abscisic acid (ABA)-synthesizing gene 9-cis-epoxycarotenoid dioxygenase 3 (OsNCED3) in the alkaline-resistant rice cultivar Dongdao-4 to generate three transgenic lines (OE-1, -2, and -3). These transgenic lines exhibited enhanced root phenotypes and increased tolerance to alkaline stress compared to wild-type (WT) plants. The content of ABA and activity of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX), were significantly higher in the transgenic lines, whereas the levels of reactive oxygen species (ROS) (O2·- and H2O2) and malondialdehyde (MDA) were reduced in the transgenic lines under hydroponic alkaline stress conditions. Transcriptome analysis of the roots under 15 mmol L-1 Na2CO3 stress identified 2915 upregulated and 2070 downregulated differentially expressed genes (DEGs) between the WT and transgenic lines. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analyses of the DEGs revealed enrichment in plant hormone signal transduction and MAPK signalling pathways, suggesting a role in stress response regulation. Additionally, agronomic surveys indicated that the grain yield of OsNCED3-overexpressing lines was significantly higher than that of the WT. These findings provide a theoretical and practical foundation for improving rice alkaline tolerance and productivity in saline-alkaline soils.

Grain weight and panicle architecture are pivotal determinants of rice yield, yet the regulatory mechanisms coordinating these traits remain elusive. Here, we functionally characterized a phytochrome-interacting factor, OsPIL11, serving as a negative regulator of grain weight and grain number per panicle. Knocking out OsPIL11 resulted in increased grain weight and grain number per panicle. OsPIL11 regulates grain weight by affecting cell expansion and division in the spikelet hulls, and controls grain number per panicle by regulating the number of primary branches. We further identified MicroRNA530, and cytokinin oxidase/dehydrogenase 2 as the target genes of OsPIL11 to regulate grain size and grain number in rice. Analysis of genetic variations suggested that there are two main haplotypes (Hap1 and Hap2) of OsPIL11. Hap1 confers the increased grain width and grain weight compared to Hap2, implying Hap1 as a superior haplotype for yield improvement. These findings provide novel insights into the molecular mechanisms underlying the regulation of rice yield, offering valuable genetic resources for the development of high-yield rice varieties through molecular breeding approaches.

Salinity is an environmental stress that severely impacts rice grain yield and quality. However, limited information is available on the molecular mechanism by which salinity reduces grain quality. In this study, we investigated the milling, appearance, eating and cooking, and nutritional quality among three japonica rice cultivars grown either under moderate salinity with an electrical conductivity of 4 dS/m or under non-saline conditions in a paddy field in Dongying, Shandong, China. Moderate salinity affected rice appearance quality predominantly by increasing chalkiness rate and chalkiness degree and affected rice eating and cooking and nutritional quality predominantly by decreasing amylose content and increasing protein content. We compared the expression levels of genes determining grain chalkiness, amylose content, and protein content in developing seeds (0, 5, 10, 15, and 20 days after flowering) of plants grown under saline or non-saline conditions. The chalkiness-related gene Chalk5 was up-regulated and WHITE-CORE RATE 1 was repressed. The genes Nuclear factor Y and Wx, which determine amylose content, were downregulated, while protein-content-associated genes OsAAP6 and OsGluA2 were upregulated by salinity in the developing seeds. These findings suggest some target genes that may be utilized to improve the grain quality under salinity stress conditions via gene-pyramiding breeding approaches.

Oxidative stress, resulting from the excessive production of reactive oxygen species, is a common and major cause of cellular damage in plants exposed to various abiotic stresses. To address this challenge, we introduce the concept of antioxidant agriculture as a comprehensive strategy to improve stress tolerance and thus crop productivity by minimizing oxidative stress levels in the field environment. This strategy encompasses a diverse range of approaches, including genetic engineering, the exogenous application of antioxidant agents, microbial inoculation, and agronomic practices, to reinforce the plant’s intrinsic antioxidant defense system and mitigate oxidative stress. We present recent successful studies of antioxidant measures that have been validated in field conditions, along with our perspective on achieving antioxidant agriculture.

Grain yield in rice is largely determined by grain size. Grain Size 3 ( GS3 ) is a major quantitative trait locus for grain size. The C–A natural variation in the second exon of GS3 was reported to play an important role in regulating grain length in rice. Here we evaluate GS3 alleles among 303 germplasm accessions. The GS3 A allele was predominant in xian/indica (XI) accessions, whereas geng/japonica (GJ) accessions mainly carried GS3 C . The GS3 allele affected the grain length significantly in XI, while its function was minimal in GJ, indicating that introduction of GS3 alleles might be useful to modify grain length in XI breeding programs, but not in GJ breeding. The association between GS3 alleles and seed weight was not significant in any of the individual subpopulations, suggesting that the contribution of GS3 to grain weight could be slight in terms of different subspecies. To develop an effective marker for GS3 , a penta-primer amplification-refractory mutation system (PARMS) marker exploiting a single-base mutation (C–A) was developed, which entailed lower cost and less time than other available markers, and should be useful for fine marker-assisted selection of grain length in XI accessions breeding.

For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610 expression quantitative trait loci associated with the expression of 7787 and 9361 eGenes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5-a major salt-tolerant locus known as qSTS5. Intriguingly, STG5 is required for maintaining Na+/K+ homeostasis by directly regulating the transcription of multiple members of the OsHKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.

Although elevated ambient temperature causes many effects on plant growth and development, the mechanisms of plant high-ambient temperature sensing remain unknown. In this study, we show that GLYCOGEN SYNTHASE KINASE 3s (GSK3s) negatively regulate high-ambient temperature response and oligomerize upon high-temperature treatment. We demonstrate that GSK3 kinase BIN2 specifically interacts with the high-temperature sensor phytochrome B (phyB) but not the high-temperature sensor EARLY FLOWER 3 (ELF3) to phosphorylate and promote phyB photobody formation. Furthermore, we show that phosphorylation of phyB by GSK3s promotes its interaction with ELF3. Subsequently, we find that ELF3 recruits the phyB photobody facilitator HEMERA (HMR) to promote its association with phyB. Taken together, our data reveal a mechanism that GSK3s promote the phyB-ELF3-HMR complex formation in regulating plant thermomorphogenesis.

Salinity is a common abiotic stress that limits crop productivity. Although there is a wealth of evidence suggesting that miRNA and lncRNA play important roles in the response to salinity in rice seedlings and reproductive stages, the mechanism by which competing endogenous RNAs (ceRNAs) influence salt tolerance and yield in rice has been rarely reported. In this study, we conducted full whole-transcriptome sequencing of rice panicles during the reproductive period to clarify the role of ceRNAs in the salt stress response and yield. A total of 214 lncRNAs, 79 miRNAs, and 584 mRNAs were identified as differentially expressed RNAs under salt stress. Functional analysis indicates that they play important roles in GO terms such as response to stress, biosynthesis processes, abiotic stimuli, endogenous stimulus, and response to stimulus, as well as in KEGG pathways such as secondary metabolite biosynthesis, carotenoid biosynthesis, metabolic pathways, and phenylpropanoid biosynthesis. A ceRNA network comprising 95 lncRNA–miRNA–mRNA triplets was constructed. Two lncRNAs, MSTRG.51634.2 and MSTRG.48576.1, were predicted to bind to osa-miR172d-5p to regulate the expression of OsMYB2 and OsMADS63, which have been reported to affect salt tolerance and yield, respectively. Three lncRNAs, MSTRG.30876.1, MSTRG.44567.1, and MSTRG.49308.1, may bind to osa-miR5487 to further regulate the expression of a stress protein (LOC_Os07g48460) and an aquaporin protein (LOC_Os02g51110) to regulate the salt stress response. This study is helpful for understanding the underlying molecular mechanisms of ceRNA that drive the response of rice to salt stress and provide new genetic resources for salt-resistant rice breeding.

Heading date of rice (Oryza sativa) is a key factor determining rice production and regional adaptability. We analysed the molecular mechanism of OsPIL15, encoding phytochrome-interacting factor-like protein, in delaying rice heading date. Overexpression of OsPIL15 delayed rice heading date by upregulating Hd1 and inhibiting Hd3a and RFT1 expression. OsLF, encoding one rice heading repressor, was found to be the putative candidate regulated by OsPIL15 through a chromatin immunoprecipitation sequencing assay and a transcriptome sequencing assay. OsPIL15 could directly bind to the OsLF promoter and activated its expression. Knocking-out OsLF in OsPIL15-overexpressing lines resulted in flowering 2-3 days earlier, partially rescuing the delayed phenotype. This indicates that overexpression of OsPIL15 overexpression delays heading date partially through OsLF. Protein-protein interaction assay of OsPIL15 or OsPIL15-∆APB (OsPIL15 lacking the active phytochrome B [phyB]-binding [APB] motif) with PHYB showed that the APB motif was required for the interaction between OsPIL15 and PHYB. Furthermore, overexpression of either OsPIL15-∆APB in the wild type or OsPIL15 in the phyB mutant did not delay rice heading date under natural long-day conditions, suggesting that phyB influences OsPIL15-mediated delay in rice heading date.

Soil salinization and/or alkalization is a major constraint to crop production worldwide.Approximately 60％of the cultivated land is affected by salt,over half of which is alkalized.Alkaline soils are characterized by high alkalinity and typically high salinity,which creates a complex saline-alkaline(SA)stress that affects plant growth.Rice cultivation has been accepted as an important strategy for effective utilization of SA land if water is available for irrigation.Nevertheless,as a salt-sensitive plant,rice plants suffer severe SA-induced damage,which results in poor plant growth and grain yield.Various approaches have been employed to improve rice productivity in SA land.Among them,the priming technique has emerged as a powerful method for enhancing SA tolerance in rice plants.In this review,we summarized how SA stress damages rice plants,and then presented how priming treatment can mitigate such damage.