Search Results (60)

Rice grain yield and drought tolerance are critical for global food security. So far, only a few genes have been reported to regulate both traits simultaneously. Here, we characterize OsFLO1, a previously unreported FAD-linked oxidoreductase, as a dual regulator of grain development and drought stress tolerance in rice. Genome-wide association studies (GWAS) revealed natural variation in OsFLO1, with haplotypes showing geographic adaptation to local rainfall. Functional analysis demonstrated that overexpression (OX) lines exhibited larger grains and improved panicle traits, while knockout (CR) lines showed reduced grain size and yield components despite increased tiller number. Regarding drought tolerance, OX lines of OsFLO1 enhanced drought tolerance, as evidenced by increased root length and antioxidant activities, whereas knockout (CR) lines displayed impaired stress responses. We further show that OsWRKY53 directly binds the OsFLO1 promoter, thereby activating its expression and coordinating both grain development and stress responses. Together, these results suggest that OsFLO1 functions as a key regulator coordinating grain development and drought tolerance, making it a promising target for improving rice productivity. Full article

Lodging is a major constraint to rice productivity and grain quality. The mechanical strength of basal internodes, particularly bending resistance (BDR), is a critical determinant of lodging resistance. In this study, we evaluated the BDR of the third and fourth basal internodes (BDR3 and BDR4) in a diverse panel of 340 rice accessions. A genome-wide association study (GWAS) identified three QTLs significantly associated with BDR3, which were defined and designated as qBDR1, qBDR4, and qBDR5. Further analysis revealed that OsWRKY102 on qBDR1 was identified as a key candidate gene. Haplotype analysis revealed distinct allelic variations between subspecies, with the elite haplotypes (Hap.1 and Hap.4) contributing to superior lodging resistance, while Hap.2 was predominantly found in lodging-susceptible Japonica accessions. CRISPR/Cas9-mediated knockout of OsWRKY102 in the ZH11 background resulted in a significant reduction of more than 50% in both BDR3 and BDR4 compared to the wild type. Detailed phenotypic characterization of the oswrky102 mutants revealed a substantial decrease in cellulose content and culm diameter, accompanied by an increase in culm wall thickness. These findings demonstrate that OsWRKY102 maintains culm mechanical strength by promoting radial expansion and cellulose accumulation. Biomechanical analysis further suggests that culm diameter and cellulose content are more critical for bending strength than wall thickness. Our results elucidate the regulatory role of OsWRKY102 in coordinating culm morphology and cell wall composition, providing a valuable genetic target for molecular breeding of high-yielding, lodging-resistant rice varieties. Full article

Silicon (Si) serves as a beneficial element that enhances plant resistance to both abiotic and biotic stresses. Although its positive effects have been widely investigated, the molecular mechanisms by which silicon improves stress tolerance in rice (Oryza sativa L.) remain unclear. Here, we show that Si displayed an optimal improved effect at concentrations of 2–4 mM in hydroponic system, and Si enhanced rice tolerance to drought and blast disease by maintaining reactive oxygen species (ROS) homeostasis and reducing root cell damage. In addition, Si at 4 mM upregulated the ABA biosynthesis gene OsNCED3, stress- and ABA-responsive genes OsDREB2A and OsLEA5, as well as the catalase gene OsCatB, while suppressing the drought-responsive negative regulator OsWRKY5, thereby enhancing drought tolerance through an ABA-dependent signaling pathway. Si at 4 mM enhanced resistance to rice blast by activating defense-related genes OsPBZ1, OsPR10a, OsPR5 and OsWRKY45 while simultaneously boosting ROS-scavenging capacity. Collectively, our results demonstrate that Si enhances rice tolerance to drought and blast disease through the coordinated modulation of ABA signaling, ROS homeostasis, and stress-related gene expression. Full article

Cold stress poses a major threat to rice productivity and grain quality. WRKY transcription factors, one of the largest plant-specific gene families, play crucial roles in plant responses to abiotic stress. However, their functions in cold responses and the evolutionary mechanisms underlying cold adaptation during the long-term domestication of cultivated rice remain poorly understood. Here, we identified OsWRKY26 as an important regulator of cold adaptation in japonica subspecies through transcriptome sequencing (RNA-seq). Subcellular localization analysis showed that the OsWRKY26 protein is localized to the nucleus under both normal and cold-stress conditions. Expression analysis indicated that OsWRKY26 is significantly upregulated at low temperature. Moreover, transgenic validation and measurements of multiple physiological traits demonstrated that OsWRKY26 positively regulates seedling cold tolerance in rice. Evolutionary analyses of OsWRKY26 and OsMYB2, a previously reported positive regulator of rice cold tolerance, suggested that these two genes diverged in wild rice and subsequently experienced directional selection in temperate japonica cultivated in high-altitude and high-latitude regions. Together, these findings provide a theoretical foundation for dissecting cold-tolerance mechanisms in rice, as well as promising genetic resources for molecular breeding in low-temperature environments. Full article

Japonica rice is susceptible to cold stress at the booting stage, yet the systematic molecular mechanisms underlying varietal disparities in cold tolerance at this stage remain poorly understood. To fill this research gap, cold-tolerant LG1934 (V3) and cold-sensitive KD8 (V6) were subjected to low-temperature treatment (15 °C) for 0 h (T1), 72 h (T3), and 120 h (T5) at the booting stage, followed by analyses of agronomic traits, antioxidant physiology, metabolome, transcriptome, and weighted gene co-expression network analysis (WGCNA). Phenotypic results showed that low temperature was the main driver of differences in panicle length, seed setting rate, and grain weight between the two varieties, with V3 exhibiting significantly stronger cold tolerance. Under cold stress, V3 maintained higher activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), accompanied by lower O₂⁻ accumulation and higher contents of malondialdehyde (MDA), H₂O₂, and proline compared to V6. Metabolomic analysis identified 56 differential accumulated metabolites (DAMs), with amino acids and their derivatives (notably L-aspartic acid) as key contributors. RNA-seq analysis identified 472 common differentially expressed genes (DEGs) that were enriched in alanine, aspartate, and glutamate metabolism, with 20 transcription factors (TFs) from TCP, WRKY, and bHLH families screened. The WGCNA revealed nine DEM-correlated modules, with orange and pink modules positively associated with L-aspartic acid. Eleven core TFs were identified, among which OsPCF5 acted as a hub regulator that activated OsASN1 transcription to promote L-aspartate biosynthesis, enhancing ROS scavenging and cold tolerance. This study systematically demonstrated the cold tolerance molecular network in japonica rice at the booting stage, highlighting the antioxidant system and L-aspartate-mediated pathway, and the core genes provided valuable resources for cold-tolerance breeding. Full article

Transcription factors (TFs) orchestrate plant growth and development, yet the functional landscape of many TF gene families remains incomplete. Here, we systematically characterize OsWRKY7, an unannotated WRKY TF in rice. Phylogenomic analyses revealed that the WRKY7 subfamily originated in basal angiosperms and evolved under strong purifying selection. We demonstrate OsWRKY7 functions as a WRKY transcriptional activator, with its activity uniquely encoded within the N-terminal domain—a distinctive mechanism among WRKY proteins. The promoter is enriched with cis-elements responsive to hormone and stress signaling, and the gene shows predominant expression in seeds. Strikingly, haplotype analysis revealed exceptionally low genetic diversity at the OsWRKY7 locus, suggesting evolutionary constraint or a recent selective sweep. Our findings establish OsWRKY7 as a conserved regulator with unique molecular features, specifically the WRKY domain, providing a strategic target for both fundamental research and crop improvement. Full article

The document is an updated review, starting from the Special Issue “Molecular Breeding for Abiotic Stress Tolerance in Crops” published in the Int. J. Mol. Sci. It reviews molecular breeding strategies to enhance abiotic stress tolerance in crops, addressing challenges like drought, salinity, temperature extremes, and waterlogging, which threaten global food security. Climate change intensifies these stresses, making it critical to develop resilient crop varieties. Plants adapt to stress through mechanisms such as hormonal regulation (e.g., ABA, ethylene), antioxidant defense (e.g., SOD, CAT), osmotic adjustment (e.g., proline accumulation), and gene expression regulation via transcription factors like MYB and WRKY. Advanced tools, such as CRISPR/Cas9 genome editing, enable precise modifications of stress-related genes, improving tolerance without compromising yield. Examples include rice (OsRR22, OsDST) and wheat (TaERF3, TaHKT1;5). Epigenetic regulation, including DNA methylation and histone modifications, also plays a role in stress adaptation. Specific studies focused on polyamine seed priming for improved germination and stress resistance, cadmium detoxification mechanisms, and genome-wide association studies (GWAS) to identify genetic markers for salt tolerance and yield. Research on salinity tolerance in wheat emphasizes sodium exclusion and tissue tolerance mechanisms. Future perspectives focus on genetic engineering, molecular markers, epigenetic studies, and functional validation to address environmental stress challenges, including the use of AI and machine learning to manage the large amount of data. The review underscores the importance of translating molecular findings into practical applications to ensure sustainable crop production under changing climates. Full article

Background/Objectives: Low-temperature stress during the grain-filling stage negatively affects rice grain quality and yield. Understanding the physiological and molecular mechanisms underlying cold tolerance is critical for breeding rice varieties with improved resilience. Methods: In this study, eight rice varieties with differential cold tolerance—LD1603, 13108, LD18, and 4-1021 (cold-tolerant) and LD3, LD4, LD121, and LD1604 (cold-sensitive)—were subjected to 17.5 °C low-temperature stress during grain filling in a naturally illuminated phytotron. Amylose and protein content, as well as taste quality, were analyzed. RNA sequencing was performed to identify differentially expressed genes and transcription factors associated with cold response. Results: Under low-temperature stress, amylose and protein content significantly increased in all eight varieties. The taste quality of cold-sensitive varieties declined markedly, whereas cold-tolerant varieties maintained higher and more stable taste quality values. Transcriptomic analysis revealed that key enzyme genes (INV, SUS, HXK, FRK, amyA, and TPP) in the starch and sucrose metabolism pathway were significantly upregulated in cold-tolerant varieties (LD18 and 4-1021), but suppressed in cold-sensitive varieties. Several cold-responsive transcription factors from the NAC, WRKY, AP2/ERF, MYB, and bZIP families were also identified. Weighted gene co-expression network analysis (WGCNA) further revealed hub TFs (OsWRKY1, OsWRKY24, OsWRKY53, and OsMYB4) and structural genes (OsPAL04 and OsCDPK7) potentially involved in cold tolerance during grain filling. Conclusions: This study enhanced our understanding of the molecular response to low temperature during rice grain filling and provided candidate genes for developing cold-tolerant rice varieties through molecular breeding. Full article

Natural variations conferring salt tolerance (ST) are of great value for breeding salt-tolerant rice varieties. The major ST genes, including SKC1, RST1, OsWRKY53 and STG5, have been identified to contain or be associated with a specific single nucleotide polymorphism (SNP). However, the distribution and genetic effects of those ST genes in rice cultivars remain poorly understood. Here, we investigated the distribution of seven cloned ST genes, including SKC1 (P140A, R184H), RST1 (A530G, E611G), OsWRKY53 (A173G), STG5 (I12S), OsHKT1;1 (L94K), OsHKT2;3 (I77T) and OsSTL1 (P289S), which contain one or two ST-related SNPs in a sequenced Indica/Xian rice population comprising 550 accessions. On the basis of the SNPs, the population was categorized into 21 haplotypes (Haps), each of which contained at least four out of seven ST genes. To precisely evaluate each SNP, grouped rice varieties that only differed at one SNP were chosen from two Haps for salt treatment with 150 mM NaCl for 7 d. The results revealed that RST1^611G showed up to 88.6% improvement in salt tolerance considering the relative shoot fresh weight (rSFW). Alternatively, OsWRKY53^173G, OsHKT2;3^77T, SKC1^140A and SKC1^184H showed an improvement in rSFW of 38.6%, 37%, 27.5% and 19.0%, respectively, indicating that they contribute different genetic effects for ST. OsHKT1;1^94K showed no function with salt treatment for 7 d, but showed a 37.9% rSFW improvement with salt treatment for 14 d. Furthermore, we found that the expression of OsWRKY53^173G was positively correlated with SKC1 and conditionally participated in ST dependent on SKC1^140A. Interestingly, RST1^530A was previously reported to be associated with salt sensitivity, but it was found to be associated with salt tolerance in this study. Overall, our results provide further insight into the mechanism and marker-assisted selection improvement of ST in Indica/Xian rice. Full article

The banana gene MaWRKY45 gene encodes a WRKY transcription factor (TF) that is closely related to OsWRKY45, which is a master regulator of defense responses in rice. MaWRKY45 is a transcription factor with proven transactivation activity and nuclear localization. Its expression is upregulated by the defense phytohormones salicylic acid (SA) and jasmonic acid (JA). Despite these findings, its transcriptome-wide impact during overexpression remains unexplored. Accordingly, the present study employed the Infiltration-RNAseq method to identify differentially expressed genes (DEGs) resulting from the overexpression of MaWRKY45 in the leaves of the model plant Nicotiana benthamiana. A total of 2473 DEGs were identified in N. benthamiana leaves overexpressing the banana gene MaWRKY45. Of these, 1092 were up-regulated and 1381 were down-regulated. Among the genes that were found to be up-regulated, those encoding proteins that are involved in plant immunity were identified. These included disease resistance receptors, proteins that are involved in cell wall reinforcement, proteins that possess antimicrobial and insecticidal activities, and defense-related TFs. It was thus concluded that the function of the banana gene MaWRKY45 is associated with the plant immune system, and that its overexpression can lead to enhance defense responses. Full article

Rice bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a major threat to rice production and food security. Exploring new resistance genes and developing varieties with broad-spectrum and high resistance has been a key focus in rice disease resistance research. In a preliminary study, rice cultivar Fan3, exhibiting high resistance to PXO99^A and susceptibility to AH28, was developed by enhancing the resistance of Yuehesimiao (YHSM) to BB. This study performed a transcriptome analysis on the leaves of Fan3 and YHSM following inoculation with Xoo strains AH28 and PXO99^A. The analysis revealed significant differential expression of 14,084 genes. Among the transcription factor (TF) families identified, bHLH, WRKY, and ERF were prominent, with notable differences in the expression of OsWRKY62, OsWRKY76, and OsbHLH6 across samples. Over 100 genes were directly linked to disease resistance, including nearly 30 NBS–LRR family genes. Additionally, 11 SWEET family protein genes, over 750 protein kinase genes, 63 peroxidase genes, and eight phenylalanine aminolysase genes were detected. Gene ontology (GO) analysis showed significant enrichment in pathways related to defense response to bacteria and oxidative stress response. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis and diterpenoid biosynthesis pathways. Gene expression results from qRT-PCR were consistent with those from RNA-Seq, underscoring the reliability of the findings. Candidate genes identified in this study that may be resistant to BB, such as NBS–LRR family genes LOC_Os11g11960 and LOC_Os11g12350, SWEET family genes LOC_Os01g50460 and LOC_Os01g12130, and protein kinase-expressing genes LOC_Os01g66860 and LOC_Os02g57700, will provide a theoretical basis for further experiments. These results suggest that the immune response of rice to the two strains may be more concentrated in the early stage, and there are more up-regulated genes in the immune response of the high-resistant to PXO99A and medium-resistant to AH28, respectively, compared with the highly susceptible rice. This study offers a foundation for further research on resistance genes and the molecular mechanisms in Fan3 and YHSM. Full article

Biotic stressors pose significant threats to crop yield, jeopardizing food security and resulting in losses of over USD 220 billion per year by the agriculture industry. Plants activate innate defense mechanisms upon pathogen perception and invasion. The plant immune response comprises numerous concerted steps, including the recognition of invading pathogens, signal transduction, and activation of defensive pathways. However, pathogens have evolved various structures to evade plant immunity. Given these facts, genetic improvements to plants are required for sustainable disease management to ensure global food security. Advanced genetic technologies have offered new opportunities to revolutionize and boost plant disease resistance against devastating pathogens. Furthermore, targeting susceptibility (S) genes, such as OsERF922 and BnWRKY70, through CRISPR methodologies offers novel avenues for disrupting the molecular compatibility of pathogens and for introducing durable resistance against them in plants. Here, we provide a critical overview of advances in understanding disease resistance mechanisms. The review also critically examines management strategies under challenging environmental conditions and R-gene-based plant genome-engineering systems intending to enhance plant responses against emerging pathogens. This work underscores the transformative potential of modern genetic engineering practices in revolutionizing plant health and crop disease management while emphasizing the importance of responsible application to ensure sustainable and resilient agricultural systems. Full article

Soil salinization is a major factor that reduces crop yields. There are some plant growth-promoting rhizobacteria (PGPR) that can stimulate and enhance the salt tolerance of plants near their roots in saline–alkali environments. Currently, there is relatively little research on PGPR in rice saline–alkali tolerance. In the early stages of this study, a strain of Microbacterium ginsengiterrae S4 was screened that could enhance the growth of rice in a laboratory-simulated saline–alkali environment (100 mM NaCl, pH 8.5). The experiment investigated the effects of S4 bacteria on the growth, antioxidant capacity, and osmotic regulation of rice seedlings under saline–alkali stress. RNA-Seq technology was used for transcriptome sequencing and UPLC-MS/MS for metabolite detection. Research has shown that S4 bacteria affect the growth of rice seedlings under saline–alkali stress through the following aspects. First, S4 bacteria increase the antioxidant enzyme activity (SOD, POD, and CAT) of rice seedlings under saline–alkali stress, reduce the content of MDA, and balance the content of osmotic regulatory substances (soluble sugar, soluble protein, and proline). Second, under saline–alkali stress, treatment with S4 bacteria caused changes in differentially expressed genes (DEGs) (7 upregulated, 15 downregulated) and differentially metabolized metabolites (101 upregulated; 26 downregulated) in rice seedlings. The DEGs are mainly involved in UDP-glucose transmembrane transporter activity, while the differentially metabolized metabolites are mainly involved in the ABC transporters pathway. Finally, key genes and metabolites were identified through correlation analysis of transcriptomes and metabolomes, among which OsSTAR2 negatively regulates L-histidine, leading to an increase in L-histidine content. Furthermore, through gene correlation and metabolite correlation analysis, it was found that OsWRKY76 regulates the expression of OsSTAR2 and that L-histidine also causes an increase in 2-methyl-4-pentenoic acid content. Based on the above analysis, the addition of S4 bacteria can significantly improve the tolerance of rice in saline–alkali environments, which has a great application value for planting rice in these environments. Full article

Low-temperature chilling is a major abiotic stress leading to reduced rice yield and is a significant environmental threat to food security. Low-temperature chilling studies have focused on physiological changes or coding genes. However, the competitive endogenous RNA mechanism in rice at low temperatures has not been reported. Therefore, in this study, antioxidant physiological indices were combined with whole-transcriptome data through weighted correlation network analysis, which found that the gene modules had the highest correlation with the key antioxidant enzymes superoxide dismutase and peroxidase. The hub genes of the superoxide dismutase-related module included the UDP-glucosyltransferase family protein, sesquiterpene synthase and indole-3-glycerophosphatase gene. The hub genes of the peroxidase-related module included the WRKY transcription factor, abscisic acid signal transduction pathway-related gene plasma membrane hydrogen-ATPase and receptor-like kinase. Therefore, we selected the modular hub genes and significantly enriched the metabolic pathway genes to construct the key competitive endogenous RNA networks, resulting in three competitive endogenous RNA networks of seven long non-coding RNAs regulating three co-expressed messenger RNAs via four microRNAs. Finally, the negative regulatory function of the WRKY transcription factor OsWRKY61 was determined via subcellular localization and validation of the physiological indices in the mutant. Full article

JAZ proteins function as transcriptional regulators that form a jasmonic acid–isoleucine (JA-Ile) receptor complex with coronatine insensitive 1 (COI1) and regulate plant growth and development. These proteins also act as key mediators in signal transduction pathways that activate the defense-related genes. Herein, the role of OsJAZ4 in rice blast resistance, a severe disease, was examined. The mutation of OsJAZ4 revealed its significance in Magnaporthe oryzae (M. oryzae) resistance and the seed setting rate in rice. In addition, weaker M. oryzae-induced ROS production and expression of the defense genes OsO4g10010, OsWRKY45, OsNAC4, and OsPR3 was observed in osjaz4 compared to Nipponbare (NPB); also, the jasmonic acid (JA) and gibberellin4 (GA4) content was significantly lower in osjaz4 than in NPB. Moreover, osjaz4 exhibited a phenotype featuring a reduced seed setting rate. These observations highlight the involvement of OsJAZ4 in the regulation of JA and GA4 content, playing a positive role in regulating the rice blast resistance and seed setting rate. Full article