Search Results (52)

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

Leucine-rich repeat receptor-like kinases (LRR-RLKs) are an important subfamily of receptor-like kinases (RLKs) in plants that play key roles in sensing different biotic and abiotic stress. However, the role of LRR-RLKs in herbivore-induced plant defense remains largely elusive. Here, we found that the expression of a rice gene, OsRLK7-1, was induced by mechanical wounding, but was slightly suppressed by the infestation of gravid females of brown planthopper (BPH, Nilaparvata lugens) or white-backed planthopper (WBPH, Sogatella furcifera). Through targeted disruption of OsRLK7-1 (resulting in the ko-rlk lines), we observed an augmentation in transcript levels of BPH-induced OsMPK3, OsWRKY30, OsWRKY33, and OsWRKY45, alongside heightened levels of planthopper-induced jasmonic acid, JA-isoleucine, and abscisic acid in plant tissues. These dynamic changes further facilitated the biosynthesis of multiple phenolamides within the rice plants, culminating in an enhanced resistance to planthopper infestations under both lab and field conditions. In addition, knocking out OsRLK7-1 impaired plant growth and reproduction. These results suggest that OsRLK7-1 plays an important role in regulating rice growth, development, and rice-planthopper interactions. Full article

Rice is a crucial global food crop, but it lacks a natural tolerance to high salt levels, resulting in significant yield reductions. To gain a comprehensive understanding of the molecular mechanisms underlying rice’s salt tolerance, further research is required. In this study, the transcriptomic and metabolomic differences between the salt-tolerant rice variety Lianjian5 (TLJIAN) and the salt-sensitive rice variety Huajing5 (HJING) were examined. Transcriptome analysis revealed 1518 differentially expressed genes (DEGs), including 46 previously reported salt-tolerance-related genes. Notably, most of the differentially expressed transcription factors, such as NAC, WRKY, MYB, and EREBP, were upregulated in the salt-tolerant rice. Metabolome analysis identified 42 differentially accumulated metabolites (DAMs) that were upregulated in TLJIAN, including flavonoids, pyrocatechol, lignans, lipids, and trehalose-6-phosphate, whereas the majority of organic acids were downregulated in TLJIAN. The interaction network of 29 differentially expressed transporter genes and 19 upregulated metabolites showed a positive correlation between the upregulated calcium/cation exchange protein genes (OsCCX2 and CCX5_Ath) and ABC transporter gene AB2E_Ath with multiple upregulated DAMs in the salt-tolerant rice variety. Similarly, in the interaction network of differentially expressed transcription factors and 19 upregulated metabolites in TLJIAN, 6 NACs, 13 AP2/ERFs, and the upregulated WRKY transcription factors were positively correlated with 3 flavonoids, 3 lignans, and the lipid oleamide. These results suggested that the combined effects of differentially expressed transcription factors, transporter genes, and DAMs contribute to the enhancement of salt tolerance in TLJIAN. Moreover, this study provides a valuable gene–metabolite network reference for understanding the salt tolerance mechanism in rice. Full article

Drought stress is one of the major causes of crop losses. The WRKY families play important roles in the regulation of many plant processes, including drought stress response. However, the function of individual WRKY genes in plants is still under investigation. Here, we identified a new member of the WRKY families, OsWRKY97, and analyzed its role in stress resistance by using a series of transgenic plant lines. OsWRKY97 positively regulates drought tolerance in rice. OsWRKY97 was expressed in all examined tissues and could be induced by various abiotic stresses and abscisic acid (ABA). OsWRKY97-GFP was localized to the nucleus. Various abiotic stress-related cis-acting elements were observed in the promoters of OsWRKY97. The results of OsWRKY97-overexpressing plant analyses revealed that OsWRKY97 plays a positive role in drought stress tolerance. In addition, physiological analyses revealed that OsWRKY97 improves drought stress tolerance by improving the osmotic adjustment ability, oxidative stress tolerance, and water retention capacity of the plant. Furthermore, OsWRKY97-overexpressing plants also showed higher sensitivity to exogenous ABA compared with that of wild-type rice (WT). Overexpression of OsWRKY97 also affected the transcript levels of ABA-responsive genes and the accumulation of ABA. These results indicate that OsWRKY97 plays a crucial role in the response to drought stress and may possess high potential value in improving drought tolerance in rice. Full article

Unfavorable environmental conditions and climate change impose stress on plants, causing yield losses worldwide. The Indonesian pigmented rice (Oryza sativa L.) cultivars Cempo Ireng Pendek (black rice) and Merah Kalimantan Selatan (red rice) are becoming popular functional foods due to their high anthocyanin contents and have great potential for widespread cultivation. However, their ability to grow on marginal, high-salinity lands is limited. In this study, we investigated whether seed halopriming enhances salt tolerance in the two pigmented rice cultivars. The non-pigmented cultivars IR64, a salt-stress-sensitive cultivar, and INPARI 35, a salt tolerant, were used as control. We pre-treated seeds with a halopriming solution before germination and then exposed the plants to a salt stress of 150 mM NaCl at 21 days after germination using a hydroponic system in a greenhouse. Halopriming was able to mitigate the negative effects of salinity on plant growth, including suppressing reactive oxygen species accumulation, increasing the membrane stability index (up to two-fold), and maintaining photosynthetic pigment contents. Halopriming had different effects on the accumulation of proline, in different rice varieties: the proline content increased in IR64 and Cempo Ireng Pendek but decreased in INPARI 35 and Merah Kalimantan Selatan. Halopriming also had disparate effects in the expression of stress-related genes: OsMYB91 expression was positively correlated with salt treatment, whereas OsWRKY42 and OsWRKY70 expression was negatively correlated with this treatment. These findings highlighted the potential benefits of halopriming in salt-affected agro-ecosystems. Full article

It has been well documented that an infestation of the piercing–sucking herbivore, brown planthopper (BPH), Nilaparvata lugens, activates strong local defenses in rice. However, whether a BPH infestation elicits systemic responses in rice remains largely unknown. In this study, we investigated BPH-induced systemic defenses by detecting the change in expression levels of 12 JA- and/or SA-signaling-responsive marker genes in different rice tissues upon a BPH attack. We found that an infestation of gravid BPH females on rice leaf sheaths significantly increased the local transcript level of all 12 marker genes tested except OsVSP, whose expression was induced only weakly at a later stage of the BPH infestation. Moreover, an infestation of gravid BPH females also systemically up-regulated the transcription levels of three JA-signaling-responsive genes (OsJAZ8, OsJAMyb, and OsPR3), one SA-signaling-responsive gene (OsWRKY62), and two JA- and SA- signaling-responsive genes (OsPR1a and OsPR10a). Our results demonstrate that an infestation of gravid BPH females systemically activates JA- and SA-dependent defenses in rice, which may in turn influence the composition and structure of the community in the rice ecosystem. Full article

Modeling biological processes and genetic-regulatory networks using in silico approaches provides a valuable framework for understanding how genes and associated allelic and genotypic differences result in specific traits. Submergence tolerance is a significant agronomic trait in rice; however, the gene–gene interactions linked with this polygenic trait remain largely unknown. In this study, we constructed a network of 57 transcription factors involved in seed germination and coleoptile elongation under submergence. The gene–gene interactions were based on the co-expression profiles of genes and the presence of transcription factor binding sites in the promoter region of target genes. We also incorporated published experimental evidence, wherever available, to support gene–gene, gene–protein, and protein–protein interactions. The co-expression data were obtained by re-analyzing publicly available transcriptome data from rice. Notably, this network includes OSH1, OSH15, OSH71, Sub1B, ERFs, WRKYs, NACs, ZFP36, TCPs, etc., which play key regulatory roles in seed germination, coleoptile elongation and submergence response, and mediate gravitropic signaling by regulating OsLAZY1 and/or IL2. The network of transcription factors was manually biocurated and submitted to the Plant Reactome Knowledgebase to make it publicly accessible. We expect this work will facilitate the re-analysis/re-use of OMICs data and aid genomics research to accelerate crop improvement. Full article

The application of Trichoderma is a form of biological control that has been effective in combating Xanthomonas oryzae pv. oryzae, the causative agent of the devastating disease known as bacterial blight of rice. In this present study, four strains of Trichoderma, viz., T. paraviridescens (BDISOF67), T. erinaceum (BDISOF91), T. asperellum (BDISOF08), and T. asperellum (BDISOF09), were collected from the rice rhizosphere and used to test their potentiality in reducing bacterial blight. The expression patterns of several core defense-related enzymes and genes related to SA and JA pathways were studied to explore the mechanism of induced resistance by those Trichoderma strains. The results primarily indicated that all Trichoderma were significantly efficient in reducing the lesion length of the leaf over rice check variety (IR24) through enhancing the expression of core defense-related enzymes, such as PAL, PPO, CAT, and POD activities by 4.27, 1.77, 3.53, and 1.57-fold, respectively, over control. Moreover, the results of qRT-PCR exhibited an upregulation of genes OsPR1, OsPR10, OsWRKY45, OsWRKY62, OsWRKY71, OsHI-LOX, and OsACS2 after 24 h of inoculation with all tested Trichoderma strains. However, in the case of RT-PCR, no major changes in OsPR1 and OsPR10 expression were observed in plants treated with different Trichoderma strains during different courses of time. Collectively, Trichoderma induced resistance in rice against X. oryzae pv. oryzae by triggering these core defense-related enzymes and genes associated with SA and JA pathways. Full article

Rice is the primary staple food for half the world’s population. Climate change challenges and food insecurity supports the need for rice with agronomically advantageous traits. We report on a transposon insertional rice mutant with enhanced germination rates. This trait is advantageous for rice growth in limited water regions and to reduce yield constraints caused by weed and bird competition. Evaluations of vital nutritional components, compositional analysis, and comparative metabolomics on threshed grain samples are performed, as these assays are those used to assess the safety of foods from genetically modified crops. Compared with the wild type (cv. Nipponbare), oswrky71 mutant grains have a similar size, shape, amount of crude fiber, crude fat, and ash content but higher crude protein. Mineral analyses reveal higher contents of phosphorus and zinc but lower calcium, potassium, sodium, and manganese in the mutant. Analysis of B vitamins reveals significantly higher riboflavin concentrations but lower choline chloride, calcium pantothenate, and thiamine. In addition, untargeted metabolomics analyses identify approximately 50 metabolites whose levels differed between the mutant and its wild type. Physical traits and compositional parameters analyzed are mostly similar and within the range or very close to being considered safe for consumption by the International Life Sciences Institute Crop Composition Database. Further agronomic evaluation and cooked rice sensory properties assessment are needed before positioning this mutant for human consumption. Full article