Rice最新文献

{"title":"A K⁺-Efflux Antiporter is Vital for Tolerance to Salt Stress in Rice.","authors":"Wei Xie, He Liu, Deyong Ren, Yiting Wei, Ying Liu, Luyao Tang, Chaoqing Ding, Zhengji Shao, Qian Qian, Yuchun Rao","doi":"10.1186/s12284-025-00815-2","DOIUrl":"10.1186/s12284-025-00815-2","url":null,"abstract":"<p><p>Salt damage significantly affects rice growth and development, posing a threat to food security. Understanding the mechanisms underlying rice's response to salt stress is crucial for enhancing its tolerance. This study aimed to elucidate the genetic and physiological mechanisms of rice adaptation to salt stress. We found that the expression of OsKEA1, a potassium (K⁺)-efflux antiporter gene in rice, was induced by salt. Both genetic and physiological experiments demonstrated that the mutation in OsKEA1 disrupted the Na⁺/K⁺ balance under salt stress conditions. Furthermore, OsKEA1 mutation exacerbated reactive oxygen species (ROS) accumulation, disrupted the antioxidant enzyme system, and compromised chloroplast integrity under salt stress. This study unveils the adaptive mechanisms of rice to salt damage and highlights the critical role of OsKEA1 in managing salt stress.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"57"},"PeriodicalIF":4.8,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Rice-Microbe Nexus: Unlocking Productivity Through Soil Science.","authors":"Aiman Hakim Bin Aminurrasyid, Asmuni Mohd Ikmal, Kalaivani K Nadarajah","doi":"10.1186/s12284-025-00809-0","DOIUrl":"10.1186/s12284-025-00809-0","url":null,"abstract":"<p><p>Rice is a staple crop and a primary food source for nearly half of the global population. Its cultivation is heavily dependent on irrigation systems, which is crucial in determining productivity. Beyond irrigation, the genetic characteristic of rice significantly influences its growth, resilience, and yield. These factors are closely connected to the soil microbiome within the rhizosphere, where interactions between plants, soil, and microbes occur, ultimately affecting agricultural outcomes. Different rice genotypes and agricultural practices shape soil microbiomes uniquely, impacting crop resilience and yield. Additionally, the growth stage of rice influences root exudation patterns, which in turn affects the composition and functionality of the rhizospheric microbiome. As the plant matures, the quantity and quality of root exudates evolve alongside its physiological changes, further modifying microbial communities in the surrounding soil. This review explores the complex interplay among irrigation strategies, rice genotypes, and growth phases, examining their collective impact on soil microbial diversity, offering insights into leveraging soil microbiomes for sustainable crop management and enhanced production. In addition it also highlights biotechnological tools and approaches that may be utilized in sustainable rice farming.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"56"},"PeriodicalIF":4.8,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12181497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144333808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Facilitating Phloem-Mediated Iron Transport Can Improve the Adaptation of Rice Seedlings to Iron Deficiency Stress.","authors":"Yan Lin, Bingjie Liu, Yuxiang Hu, Ganghua Li, Zhenghui Liu, Yanfeng Ding, Lin Chen","doi":"10.1186/s12284-025-00816-1","DOIUrl":"10.1186/s12284-025-00816-1","url":null,"abstract":"<p><p>Iron (Fe) is essential for normal plant growth and development. In rice, Fe deficiency leads to stunted growth, leaf chlorosis, reduced photosynthetic capacity, and ultimately, yield loss. Most studies have focused on investigating the mechanisms of Fe deficiency responses in rice roots; however, the effects of shoot Fe redistribution on Fe deficiency response remain poorly understood. Phloem transport plays a vital role in distributing Fe to new tissues. To investigate the effects of enhanced phloem-mediated Fe transport on rice adaptability to iron deficiency, we subjected transgenic lines with higher phloem Fe efflux rates and wild-type (WT) plants to Fe-deficient conditions. The growth, leaf photosynthetic rate, and Fe content of transgenic and WT seedlings under different Fe concentrations were compared. The results showed that the transgenic lines exhibited elevated shoot length, root length, shoot dry weight, leaf chlorophyll content, and net photosynthetic rates under Fe-deficient conditions. Under both Fe-sufficient and Fe-deficient conditions, the transgenic lines had significantly higher Fe content, Fe accumulation, and phloem Fe efflux rates than the WT. RNA sequencing (RNA-seq) analysis revealed that enhanced Fe transport via phloem resulted in improved Fe availability through the sequestration of Fe ions and vacuolar transport pathways in the shoots. It also upregulated the EARLY LESION LEAF 1 (ELL1) expression and modulated the sucrose synthase activity, thereby promoting chlorophyll synthesis and leaf photosynthesis. Additionally, enhanced Fe transport influenced the gibberellin (GA) catabolism and plant hormone signal transduction in the roots, reducing the GA content and modulating the cytokinin (CTK), jasmonic acid (JA), and ethylene (ETH) signaling to induce Fe deficiency response and promote Fe uptake. These findings demonstrate that phloem-mediated Fe transport participated in Fe deficiency response, and enhancing this improved the adaptability of rice seedlings to low Fe conditions. In specific, rice seedlings with a high capacity for phloem-mediated Fe transport exhibited a strong iron uptake, translocation, and remobilization capacity, thereby maintaining normal growth and development and successfully adapting to the low-Fe environment.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"54"},"PeriodicalIF":4.8,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12179029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144326797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"WOX11-OsPRX130 module confers rice drought tolerance by maintaining ROS homeostasis in rice root.","authors":"Mingfang Tan, Yijie Wang, Yu Zhao","doi":"10.1186/s12284-025-00800-9","DOIUrl":"10.1186/s12284-025-00800-9","url":null,"abstract":"<p><p>Plants have evolved sophisticated mechanisms to cope with drought stress. A resilient root system, coupled with appropriate levels of reactive oxygen species (ROS), is crucial for optimal growth and increased yield under drought stress. Accumulating studies have shown a strong link between root development, ROS, and drought tolerance. WOX11, as a master regulator of crown root (CR) development in rice, also governs root redox metabolism. However, it remains unknown whether WOX11 modulates ROS homeostasis in roots to facilitate adaptation to drought stress. In this study, we found that WOX11 directly binds to the promoter of the peroxidase gene OsPRX130, thereby enhancing drought tolerance by regulating CR growth. Notably, OsPRX130 is predominantly expressed in rice roots and its expression is induced by drought stress. Knockout of OsPRX130 inhibited CR growth by reducing ROS levels, ultimately compromising the drought tolerance in rice. Taken together, our findings shed light on the mechanism by which WOX11 mediates ROS accumulation through modulating the class III peroxidase gene OsPRX130 during rice CR development. This provides new insights into the functions of PRX genes during CR development. More importantly, our results deepen our understanding of how WOX11 regulates root development to enhance drought tolerance in rice and provide an alternative breeding strategy using WOX11 to control root system architecture for developing crop varieties with high drought adaptability.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"55"},"PeriodicalIF":4.8,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12179048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144326798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the Strategies of Male Sterility for Hybrid Development in Hexaploid Wheat: Prevailing Methods and Potential Approaches.","authors":"Muhammad Abdullah, Usama Sheraz, Arisha Tul Ain, Bisma Nasir, Sardar Hammad, Sajid Shokat","doi":"10.1186/s12284-025-00807-2","DOIUrl":"10.1186/s12284-025-00807-2","url":null,"abstract":"<p><p>Hybrid breeding has emerged as a pivotal strategy to enhance wheat crop yield, a critical step to meet the escalating food demand for the growing global population. Heterosis in wheat can boost crop yield; however, harnessing heterosis in bread wheat is complex and hindered by the species' inherent tendency for self-pollination, high genome ploidy, and limitation of male sterile lines. In contrast, the availability of genetic male sterility, and altering reproductive biology such as anther extrusion and floret opening, is challenging but could facilitate outcrossing. Despite the advancements in sterility systems and molecular tools, an efficient and environmentally stable wheat hybrid production system is still lacking. In this review, we examine the advantages and limitations of different male sterility sources utilized to date including, chemical hybridizing agents (CHAs), cytoplasmic male sterility (CMS), nuclear genic male sterility (NGMS), and environmental-sensitive male sterility (ESMS). Furthermore, we explore the potential of molecular tools such as marker-assisted selection (MAS), genome editing, and other genetic engineering approaches to accelerate hybrid wheat breeding efforts. Future research directions are proposed to develop robust, cost-effective systems by integrating conventional and molecular approaches with advanced screening methods including cytogenomics and next generation sequencing (NGS), which can reliably help to produce stable, high-yielding, and resilient hybrid wheat cultivars compared to current open-pollinated varieties. Collectively, these efforts are vital to achieve the food demands for escalating population under climate change scenario.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"53"},"PeriodicalIF":4.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12177127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144326796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Leucocalocybe mongolica Fungus Enhances Rice Growth by Reshaping Root Metabolism, and Hormone-Associated Pathways.","authors":"Mingzheng Duan, Ming Tao, Fuhan Wei, Honggao Liu, Sirui Han, Jieming Feng, Qiuyue Ran, Xiande Duan, Zhifang He, Shunqiang Yang, Muhammad Junaid Rao","doi":"10.1186/s12284-025-00813-4","DOIUrl":"10.1186/s12284-025-00813-4","url":null,"abstract":"<p><p>The fungal species Leucocalocybe mongolica has garnered attention due to its plant growth-promoting capabilities without fertilizers and emerged as a significant subject of research offering promising applications in sustainable agricultural practices. This study investigated the effects of LY9-transformed soil on rice growth and development through physiochemical, phenotypic, transcriptomic, and metabolomic analyses. Soil treated with varying concentrations of LY9 (10%, 30%, and 50%) exhibited significant improvements in nutrient availability compared to untreated controls. Rice plants grown in LY9-transformed soil enhanced phenotypic characteristics, including increased tillering (up to 20.29 tillers vs. 9 in control), greater root length (52.5 cm vs. 42 cm), and elevated chlorophyll content (1.21 mg/g vs. 0.38 mg/g). Transcriptomic analysis revealed significant alterations in genes related to primary and secondary metabolism, with 2,612 upregulated and 3,419 downregulated genes. KEGG pathway analysis highlighted modifications in nitrogen metabolism (24 genes), photosynthesis (41 genes), hormone signaling and tillering (222 genes), and cell wall and amino acids biosynthesis (365 genes). LC-MS/MS metabolomic profiling identified substantial increases in key amino acids, alkaloids, and phytohormones in LY9-treated rice roots. Notably, tryptophan and its derivatives showed more than 2-fold increases, suggesting enhanced auxin biosynthesis potential. The study revealed intricate molecular mechanisms underlying LY9-mediated growth promotion, particularly through modulation of nitrogen metabolism and hormone signaling pathways. These findings demonstrate the potential of LY9 as a sustainable soil amendment for improving rice productivity and provide valuable insights into the molecular basis of plant-fungal interactions in agricultural systems.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"52"},"PeriodicalIF":4.8,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170973/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144302799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GWAS Combined with Meta-Analysis Identifies OsDREB6 as a Regulator of Coleoptile Elongation Under Anaerobic Conditions in Rice.","authors":"Kai Liu, Dandan Li, Jinrui Li, Shiyi Chen, Di Zhu, Min Guo, Jing Yang, Xueyu Liang, Jiafeng Wang, Hui Wang, Chun Chen, Tao Guo, Yongzhu Liu","doi":"10.1186/s12284-025-00812-5","DOIUrl":"10.1186/s12284-025-00812-5","url":null,"abstract":"<p><p>Identifying genes resistant to anaerobic germination can provides key genetic targets for breeding direct seeding rice varieties with anaerobic tolerance. In this study, genome-wide association analysis (GWAS) was performed on coleoptile length (CL) of 591 natural rice populations under anaerobic conditions, and a total of 34 significant QTLs were identified, with eight of them co-localized with previous studies. Furthermore, through meta-analysis of 156 initial QTLs from 21 independent studies related to anaerobic germination, 37 MQTLs were identified, including 4 core MQTLs. Integration of GWAS with meta-analysis revealed the overlap between the physical interval of qCL9.5 on chromosome 9 and MQTL9.2, highlighting it as a reliable locus. Notably, our analysis pinpointed the dehydration-responsive element-binding protein 6 gene, OsDREB6, as a potential regulator impacting anaerobic germination in rice seeds. Phenotypic analysis revealed that the ko-osdreb6-1 and ko-osdreb6-2 mutants exhibited significantly increased CL and germination sprout length under aerobic treatment for 4 days compared to WT. In contrast, disruption of OsDREB6 caused reduced CL in plants seeds under under anaerobic 4-day treatment and anaerobic 3-day treatment after seed dehiscence. Additionally, the relative coleoptile lengths of the mutants after 4 days between anaerobic and aerobic treatments were significantly lower than those of WT. RNA-seq and MapMan analysis of the ko-osdreb6-1 suggested that OsDREB6 may regulate the coleoptile elongation under anaerobic conditions by affecting the expression of related genes involved in the sucrose and starch metabolism. Overall, our study demonstrated that the effectiveness of combining GWAS with meta-analysis of QTL in identifying genetic loci and key genes for improving anaerobic germination tolerance in direct seeding rice breeding.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"51"},"PeriodicalIF":4.8,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144302798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omics-Based Construction of ncRNA-Gene-Metabolite Networks Provides New Insights Into Metabolic Regulation Under Salt Stress in Rice.","authors":"Haiyang Tong, Chao Wang, Xiaoqian Han, Qihao Sun, Enxi Luo, Chao Yang, Guo Xu, Xumin Ou, Shixuan Li, Jianing Zhang, Jun Yang","doi":"10.1186/s12284-025-00811-6","DOIUrl":"10.1186/s12284-025-00811-6","url":null,"abstract":"<p><p>Rice (Oryza sativa L.), one of the most vital staple crops globally, suffers severe yield losses due to metabolic dysregulation under salt stress. However, the systemic mechanisms by which non-coding RNAs (ncRNAs) coordinately regulate metabolic reprogramming remain elusive, and the genotype-specific regulatory networks in salt-tolerant cultivars are poorly characterized. To address this, we performed metabolomic analysis using ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) across different rice varieties under salt stress, identifying 327 metabolites, with the most notable fluctuations observed in lipids, polyamines, and phenolamides. The salt-tolerant variety Pokkali exhibited 51.96% and 31.37% fewer differentially accumulated metabolites (DAMs) in the shoots and roots respectively, compared to the salt-sensitive variety Nipponbare (NIP), which explains its superior salt-tolerant phenotype from a metabolic homeostasis perspective. Transcriptome profiling revealed 18,597 differentially expressed genes (DEGs), with 70.8% showing genotype-specific expression patterns. Pokkali-specific DEGs were markedly enriched in salt-responsive pathways, including reactive nitrogen species scavenging and ion compartmentalization. By integrating long non-coding RNA (lncRNA) and microRNA (miRNA) sequencing data, we constructed a four-tiered regulatory network comprising 6,201 DEGs, 458 miRNAs, 970 DElncRNAs, and 177 metabolites. In the regulatory network, Osa-miR408-3p was identified as a negative regulator of Os03 g0709300 expression. Network analysis revealed that 21 polyamine and phenolamides biosynthesis-related genes were co-regulated by eight miRNAs, each forming a feedback loop with 2-11 lncRNAs. This study constructed a four-way cascade of \"lncRNA-miRNA-mRNA-metabolite\", and proposed a new concept of ncRNA-mediated \"network regulation instead of single-gene effect\".</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"50"},"PeriodicalIF":4.8,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12165919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144286461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Co-Cultivation with Azolla Affects the Metabolome of Whole Rice Plant Beyond Canonical Inorganic Nitrogen Fertilization.","authors":"Elena Consorti, Alma Costarelli, Sara Cannavò, Martina Cerri, Maria Cristina Valeri, Lara Reale, Antonietta Saccomanno, Chiara Paleni, Veronica Gregis, Martin M Kater, Federico Brilli, Francesco Paolocci, Andrea Ghirardo","doi":"10.1186/s12284-025-00788-2","DOIUrl":"10.1186/s12284-025-00788-2","url":null,"abstract":"<p><p>Azolla spp. are floating ferns used for centuries as biofertilizers to enrich the soil with inorganic nitrogen and improve rice yields. However, the molecular interactions between Azolla and co-cultivated rice plants only recently started to be thoroughly investigated. In this study, we exploited an experiment in which rice plants were grown together with Azolla by maintaining a low and constant concentration of inorganic nitrogen. We employed a combination of non-targeted metabolomics, chemometrics, and molecular networking to dissect the impact of Azolla co-cultivation on the metabolome of rice roots- and leaves, as well as to annotate the metabolites released by Azolla into the growing medium. Our analyses showed that Azolla can synthesize and release a broad range of metabolites in the culture medium, mainly comprising small peptides (i.e., di- and tri-peptides) and flavonoids, that may have stimulated the rice plant growth. We also observed a systemic response in the upregulation of rice metabolites, first in the roots and then in the leaves. Metabolomics analysis indicated that during the first stages of co-cultivation, the impact of Azolla on rice mainly resulted in the accumulation of small peptides, lipids and carbohydrates in roots, as well as flavonoid glycosides and carbohydrates in leaves. Consistent with these results, transcriptomics analysis of rice roots indicated significant changes in the expressions of genes coding for small peptide and lipid transporters and genes involved in the pathways of amino acid salvage and biosynthesis. Overall, our study provides new insights into Azolla's beneficial and growth-promoting effects on rice. Understanding the molecular mechanisms by which Azolla functions as a biostimulant in rice co-culture will facilitate the development of more sustainable and environmentally friendly techniques to increase yields.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"49"},"PeriodicalIF":4.8,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12149377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144249387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome Analysis Between Parents and Offspring Revealed the Early Salt Tolerance Mechanism of Rice NGY1.","authors":"Cheng Li, Kai Lu, Wen-Hua Liang, Tao Chen, Shu Yao, Lei He, Xiao-Dong Wei, Ling Zhao, Li-Hui Zhou, Chun-Fang Zhao, Qing-Yong Zhao, Zhen Zhu, Cai-Lin Wang, Ya-Dong Zhang","doi":"10.1186/s12284-025-00802-7","DOIUrl":"10.1186/s12284-025-00802-7","url":null,"abstract":"<p><p>Salt stress poses a severe threat to global rice productivity, and developing salt-tolerant cultivars represents a critical strategy to address this challenge. However, the molecular mechanisms underlying salt tolerance in rice remain elusive. This study focuses on NGY1, a crossbred offspring between YF47 and SN9903, which showed superior salt tolerance compared to its parent lines during the seedling stage. RNA sequencing (RNA-seq) of seedlings harvested at distinct temporal stages of salt stress identified over 10,000 differentially expressed genes (DEGs). Functional enrichment analyses (GO and KEGG) revealed that NGY1 uniquely mobilized a broader repertoire of stress-responsive genes within shorter timeframes than its parents lines, particularly those associated with redox homeostasis, phytohormone signaling, and MAPK cascades. Meanwhile, NGY1 can rapidly upregulate genes related to salt tolerance compared to its parent during the initial stress phase. Additionally, differences in salt tolerance between NGY1 and its parents were linked to variations in alternative splicing and the high expression of certain NBS-LRR protein genes early in salt stress exposure. These findings not only provide new insights into the molecular mechanisms of salt tolerance, but also provide a theoretical basis for genetic improvement of salt tolerance in rice.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"48"},"PeriodicalIF":4.8,"publicationDate":"2025-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12145368/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144249438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}