Plant Science最新文献

{"title":"Phenylalanine-driven metabolic induced resistance activates phenylpropanoid defenses in tomato against Tetranychus urticae.","authors":"Dayakar Boddupally, Rinat Ovadia, Rachel Davidovich-Rikanati, Stalin Nadarajan, Varun Kumar, Yigal Elad, Michal Oren-Shamir","doi":"10.1016/j.plantsci.2026.113523","DOIUrl":"10.1016/j.plantsci.2026.113523","url":null,"abstract":"<p><p>Tetranychus urticae (Koch), the two-spotted spider mite (TSSM), is a highly polyphagous agricultural pest, infesting more than 1100 plant species. Chemical control of TSSM is limited by the rapid development of resistant mite populations. Previous studies have shown that exogenous application of phenylalanine to plants is efficiently absorbed and metabolized into phenylpropanoids, thereby enhancing plant resistance to fungal and insect pests. Here, we demonstrate that phenylalanine treatment also increases plant resistance to TSSM. In choice assays, mites preferentially colonized non-treated plants over treated plants. In no-choice experiments, phenylalanine-treated plants constituted a hostile environment for TSSM: mites attempted to leave treated leaflets, exhibited increased oviposition, and showed a reduced rate of development from nymphs to mature adults. Three mechanisms underlying phenylalanine-induced resistance have previously been identified, including the accumulation of metabolites toxic to pathogens, the induction of a priming effect that enables rapid and targeted activation of plant defense genes following infection, and enhanced immunity in neighboring untreated plants. Here we present an additional mechanism involving metabolomic induced resistance, in which phenylalanine treatment triggers an early and enhanced accumulation of phenylpropanoids associated with plant immunity. These metabolites accumulate gradually in non-treated plants following TSSM infestation, ultimately reaching levels comparable to those observed in phenylalanine-treated plants. These findings demonstrate that phenylalanine accelerates the deployment of defense-associated metabolites and enhances resistance to arthropod pests.</p>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":" ","pages":"113523"},"PeriodicalIF":4.6,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149183749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and functional characterization of floral transition-related SPL genes in Pleioblastus pygmaeus.","authors":"Yao Wenjing, Li Yifang, Wei Ziye, Wu Hongyu, Gu Hongyue, Tan Qin, Lin Shuyan","doi":"10.1016/j.plantsci.2026.113517","DOIUrl":"10.1016/j.plantsci.2026.113517","url":null,"abstract":"<p><p>Floral transition has consistently remained a focal point in bamboo plants due to their unique reproductive characteristics. SPL (SQUAMOSA promoter binding protein-like) gene family encodes a class of plant-specific transcription factors (TFs) that fulfill diverse biological functions throughout the plant life, with particular prominence in phase transition. However, their functional roles and regulatory modes remain poorly understood in bamboo plants, as previous work has been confined to transcriptomic profiling and phylogenetic analyses without experimental corroboration. In this study, we identified six SPL candidates potentially involved in floral transition and flower organ development from an ornamental ground-cover bamboo species, Pleioblastus pygmaeus. Notably, four of these, namely PpSPL12, PpSPL13, PpSPL14 and PpSPL16, have been experimentally validated as direct targets of miR156a in our previous work. Tissue-specific expression profiling revealed distinct spatial patterns among the six PpSPLs, which were predominantly expressed in the different developmental stages of flowering P. pygmaeus. The transgenic rice overexpressing each of the six PpSPLs consistently exhibited delayed heading dates. Moreover, overexpression of the four miRNA156-targeted PpSPLs significantly altered vegetative growth of transgenic rice, manifested as decreased plant height and fewer tillers. Similarly, the transgenic Arabidopsis overexpressing the four miR156-targeted PpSPLs exhibited significantly delayed bolting and reduced rosette leaf numbers. Furthermore, several key flowering-promoting genes were quantified to be significantly repressed, whereas a few flowering inhibitory genes were substantially induced in these transgenic plants. In conclusion, results from heterologous overexpression of miR156-targeted PpSPLs in the model plants reveal their functional potential and divergence in both reproductive and vegetative growth, which provides theoretical basis for enriching and deepening bamboo developmental biology.</p>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":" ","pages":"113517"},"PeriodicalIF":4.6,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149183520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single nucleotide substitution in the CsDET2 gene leads to complex alterations in plant architecture and affects brassinosteroid profile in cucumber (Cucumis sativus L.).","authors":"Renata Słomnicka, Szymon Mużacz, Karolina Kaźmińska, Jana Oklestkova, Aneta Basińska-Barczak, Maciek Adamowski, Agnieszka Ostrowska, Robert Malinowski, Grzegorz Bartoszewski","doi":"10.1016/j.plantsci.2026.113519","DOIUrl":"10.1016/j.plantsci.2026.113519","url":null,"abstract":"<p><p>Most cucumber (Cucumis sativus L.) cultivars are characterized by indeterminate and vigorous growth, which requires a large cultivation area and increased labor for crop maintenance. Manipulating plant architecture may help optimize cucumber production in certain cultivation systems. The objective of this study was to identify the gene associated with phenotypic changes of the short petiole-2 (sp-2) mutant, which was discovered from EI (ethylenimine)-induced mutagenesis population. The line carrying the sp-2 gene was characterized by dwarf growth and dark-green wrinkled leaves with short petioles, while maintaining fertility and reproductive capacity. Genome-wide mapping using the F_2:3 population developed from a cross between line B10DH, characterized by an indeterminate type of growth and undisturbed leaf and petiole development, and the line sp-2, revealed that a single nucleotide substitution in the cucumber ortholog of DE-ETIOLATED 2 (CsDET2), encoding 5α-steroid reductase, one of the early step enzymes in the brassinosteroid biosynthesis pathway, is responsible for the line sp-2 phenotype. Observed change in CsDET2 results in arginine-to-tryptophan substitution in the conserved CsDET2 C-terminal reductase domain. Since brassinosteroids are involved in numerous aspects of plant development, the change in a catalytic domain of a key factor involved in BR metabolism resulted in feedback effects that could be observed as deregulation of other genes involved in BR biosynthesis, as well as profound changes in the accumulation of particular BR forms in the sp-2 line. Our study reveals a role of CsDET2 in shaping plant architecture and demonstrates how a single-nucleotide change can disrupt BR biosynthesis and alter plant growth habit.</p>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":" ","pages":"113519"},"PeriodicalIF":4.6,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149183931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long Hypocotyl 1 mediates nitrogen regulation of flowering time and nitrogen use efficiency","authors":"Xingliang Duan ,&nbsp;Guanjie Wang ,&nbsp;Qinglin Song ,&nbsp;Jiale Liu ,&nbsp;Huilin Ding ,&nbsp;Jing Che ,&nbsp;Wei Xuan","doi":"10.1016/j.plantsci.2026.113062","DOIUrl":"10.1016/j.plantsci.2026.113062","url":null,"abstract":"<div><div>Flowering time is of great significance for crop yield, reproduction and regional adaptability, which is regulated by complex gene network and environmental signals, such as nitrogen (N) nutrition. <em>Long hypocotyl 1 (HY1)</em> encodes a heme oxygenase, which is necessary for the biosynthesis of phytochrome chromophore biosynthesis, and promotes photomorphogenesis in plants. It has been reported that <em>HY1</em> regulates rice flowering time, though the molecular mechanism remains elusive. Meanwhile, whether <em>HY1</em> involves in N-regulated flowering is also unclear. Here, we found that <em>HY1</em> knock-out mutant showed early flowering and decreased grain yield. <em>HY1</em> is highly expressed in young rice leaf tissues, and its expression is induced by both light and N supply. We also revealed that <em>HY1</em> follows a circadian rhythm, and alters the expression of circadian-clock genes to regulate following time. In rice, high N supply delayed flowering time, while the flowering time of <em>hy1</em> mutant is insensitive to N supply in comparison to WT. Furthermore, <em>HY1</em> knock-out decreases N uptake and use efficiency at both low N and high N levels under long-day conditions. These results suggested a critical role of <em>HY1</em> in N-dependent signaling to regulate the function of clock and thus flowering under long-day conditions.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113062"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146228221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fvchli deficiency impairs ABA-mediated stomatal closure and enhances susceptibility to Xanthomonas fragariae in strawberry","authors":"Jingnan Luo ,&nbsp;Jiangsong Jin ,&nbsp;Yangyang Ma ,&nbsp;Yanwen Jiang ,&nbsp;Fengxue Zhu ,&nbsp;Lanyan Zhang ,&nbsp;Yingqiang Wen ,&nbsp;Jiayue Feng","doi":"10.1016/j.plantsci.2026.113068","DOIUrl":"10.1016/j.plantsci.2026.113068","url":null,"abstract":"<div><div>The magnesium chelatase subunit CHLI is well-characterized in chlorophyll biosynthesis, but its role in plant immunity remains unclear. In this study, we generated chimeric <em>Fvchli</em> mutant strawberries via CRISPR/Cas9 and obtained T1-T3 progeny with a wide range of editing efficiencies through self-pollination. Mutants with higher editing efficiency exhibited more leaf spots. Following inoculation with <em>Xanthomonas fragariae</em>, <em>Fvchli</em> mutants showed increased susceptibility, with both lesion area and disease incidence positively correlating with editing efficiency. We further demonstrated that stomata in <em>Fvchli</em> mutants closed significantly more slowly in response to ABA compared to the WT. After 1.5 h of ABA treatment, the stomatal aperture (width-to-length ratio) of the wild type (WT) decreased from 32 % to 2.3 %, whereas in the mutant line with 70 % editing efficiency, it only reduced from 32 % to 16 %. In the edited plants, the expression levels of genes related to ABA biosynthesis and signal transduction were significantly lower than those in the wild type. After pathogen infection, ABA levels increased in both WT and mutant plants, but remained significantly lower in <em>Fvchli</em> mutant. Scanning electron microscopy revealed that <em>Fvchli</em> mutants had wider stomatal apertures at 5 and 12 hpi, facilitating extensive bacterial colonization, whereas WT plants effectively restricted invasion through stomatal closure. Our results reveal a previously unrecognized role for <em>Fvchli</em> in stomatal immunity, where its deficiency impairs ABA accumulation and responsiveness, compromising stomatal defense and promoting bacterial infection.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113068"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146776485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide study of the R2R3-MYB gene family and analysis of NoMYB90 promoting anthocyanin biosynthesis in watercress (Nasturtium officinale R.Br.)","authors":"Suchong Deng,&nbsp;Qiang Ding,&nbsp;Xilin Hou","doi":"10.1016/j.plantsci.2026.113071","DOIUrl":"10.1016/j.plantsci.2026.113071","url":null,"abstract":"<div><div>Watercress (<em>Nasturtium officinale</em> R.Br.) is a kind of aquatic or semi-aquatic vegetable, which is rich in a variety of metabolites beneficial to human body. The R2R3-MYB gene family plays a key role in the biosynthesis of metabolites such as anthocyanins, but has not been characterized in watercress. Here, we identified 118 R2R3-NoMYB genes in the watercress genome and classified them into 35 subgroups. High-light treatment simultaneously enhanced anthocyanin accumulation in both lateral stems and upper main stems and strongly up-regulated the expression of subgroup S6 member <em>NoMYB90</em> as well as the anthocyanin biosynthetic structural genes. Subcellular localization showed that NoMYB90 was located in the nucleus and cell membrane. Transient overexpression of <em>NoMYB90</em> in tobacco leaves promoted anthocyanin accumulation, confirming its role as a positive regulator of anthocyanin biosynthesis. Dual-luciferase assay showed that NoMYB90 transactivates the anthocyanin biosynthetic genes <em>NoCHS</em>, <em>NoF3H</em>, <em>NoDFR</em>, and <em>NoUF3GT</em>. This study presented the first genome-wide analysis of the R2R3-MYB family in watercress and identified <em>NoMYB90</em> as a positive regulator of anthocyanin biosynthesis. The findings provided a reference for further investigations of R2R3-NoMYB genes and established a foundation for the study of anthocyanin biosynthesis in watercress.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113071"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147309397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative analysis of physiology, transcriptomics, and metabolomics unveils mechanisms in soybean (Glycine max (Linn.) Merr) response to alkaline stress","authors":"Qian Li ,&nbsp;Bo Chen ,&nbsp;Ziyu Yang ,&nbsp;ChenJing Li ,&nbsp;Qing Jing ,&nbsp;Qinghong Lu ,&nbsp;Rui Ni ,&nbsp;Pengzhi Mao ,&nbsp;Li Zhang ,&nbsp;Xinyong Guo","doi":"10.1016/j.plantsci.2026.113066","DOIUrl":"10.1016/j.plantsci.2026.113066","url":null,"abstract":"<div><div>Soybean (<em>Glycine max</em> (Linn.) Merr), an important economic crop, is significantly impacted by alkaline stress, but the regulatory networks involved under such stress remain largely unclear. This study aimed to elucidate the regulatory mechanisms of alkaline stress using alkaline-tolerant (Heihe 35) and alkaline-sensitive (Zhonghuang 911) soybean varieties, employing phenotypic, physiological, and multi-omics approaches. The results indicated that the Heihe 35 soybean variety exhibited superior growth compared to the Zhonghuang 911 variety, with increased 41.86 %-46.71 % biomass, 51.04 %-92.68 % antioxidant enzyme activity and 15.74 %-20.49 % osmotic regulators. Compared to Heihe 35, Zhonghuang 911 showed a 36.81 % higher relative conductivity, a 19.13–23.93 % increase in reactive oxygen species levels, and a 26.39 % higher malondialdehyde content. Metabolomic and transcriptomic analyses revealed that flavonoids were the most abundant metabolites in soybeans under alkaline stress, with key regulatory pathways in flavonoid, linoleic acid, and amino acid metabolism identified as crucial for the soybean response to alkaline stress. Notably, several key differential genes and metabolites showed significantly upregulated expression under alkaline stress compared to the control group, including formononetin (C00858), 9(s)-hotre (C16326), and adenine (C00147), which were upregulated by 1.65–10.56 times, as well as <em>LOC100808944</em> (K01904), <em>SDP1–4</em> (K14674), and <em>LOC100819617</em> (K01679), which were upregulated by 1.61–8.75 times. The findings of this study enhance our understanding of the physiological and molecular mechanisms underlying soybean responses to alkaline stress, highlighting the significant roles of key metabolic pathways. These insights provide a theoretical foundation for improving alkaline tolerance in soybeans and lay the groundwork for breeding alkaline-resistant varieties.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113066"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146776523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The transcription factor WRKY25 promotes seed dormancy and mediates abscisic acid signaling in Arabidopsis","authors":"Qiugui You ,&nbsp;Wanqin Chen ,&nbsp;Jinjing Pan ,&nbsp;Diqiu Yu","doi":"10.1016/j.plantsci.2026.113064","DOIUrl":"10.1016/j.plantsci.2026.113064","url":null,"abstract":"<div><div>Seed dormancy is a key adaptive trait that prevents germination under unfavorable conditions. In Arabidopsis, DELAY OF GERMINATION 1 (DOG1) serves as a master regulator of dormancy, primarily controlled through post-translational modifications. However, whether it interacts with other crucial transcriptional regulators remains to be investigated. Here, we identify WRKY25 as an interaction partner of DOG1. <em>WRKY25</em> is mainly expressed in mature seeds during seed development, and <em>wrky25</em> mutant display reduced primary dormancy, while overexpression enhances dormancy. Genetic analyses reveal that WRKY25 promotes primary seed dormancy through DOG1. Furthermore, WRKY25 modulates abscisic acid (ABA) responsiveness, as <em>wrky25</em> mutants exhibit hyposensitivity to ABA during germination and early seedling growth. Mechanistically, WRKY25 physically interacts with the core ABA signaling component ABSCISIC ACID-INSENSITIVE5 (ABI5), and genetic assays confirm ABI5's necessity for WRKY25-mediated ABA hypersensitivity. Molecular characterization establishes WRKY25 as a transcriptional activator of both DOG1 and ABI5, binding to their promoters via conserved W-box elements. Additionally, WRKY25's regulatory functions require functional DOG1 and ABI5, positioning it as a pivotal integrator of dormancy and ABA signaling pathways. Overall, our study identified WRKY25 as a regulator of seed dormancy and germination that plays a crucial role in governing these processes through the DOG1 and ABA pathways.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113064"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147309411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SmNAC68 transcription factor negatively regulate tanshinone biosynthesis under low-temperature conditions in Salvia miltiorrhiza","authors":"Gaoyang Qu ,&nbsp;Ruibo Shen ,&nbsp;Mingwan Sun ,&nbsp;Di Zhao ,&nbsp;Wei Wang ,&nbsp;Shixiang Wei ,&nbsp;Biao Wang ,&nbsp;Hongbo Li","doi":"10.1016/j.plantsci.2026.113058","DOIUrl":"10.1016/j.plantsci.2026.113058","url":null,"abstract":"<div><div><em>Salvia miltiorrhiza</em> Bge. (<em>S. miltiorrhiza</em>) is a traditional Chinese herbal medicine, primarily used for treating cardiovascular diseases. Tanshinones as the main medicinal components of <em>S. miltiorrhiza</em>, their content is an important factor affecting the medicinal and economic value. Reasonable post-harvest techniques are the critical means to improve the effective components, and short-term low-temperature can induce the synthesis of plant secondary metabolites. However, the molecular mechanisms of low-temperature regulation of tanshinones remain unclear. This study found that post-harvest low-temperature can significantly accumulate the tanshinone components, simultaneously, it markedly enhances the expression of key enzyme genes involved in tanshinone biosynthesis. Analysis of the NAC gene family revealed that <em>SmNAC68</em> is predominantly active in roots, with a marked decrease in expression under low-temperature. Genetic transformation experiments demonstrated that the accumulation of four tanshinones in <em>SmNAC68</em> overexpression individual was significantly downregulated, with the key enzyme gene <em>SmCPS1</em> showing the most significant downregulation. Protein interaction experiments revealed that <em>SmNAC68</em> can interact with the promoter of <em>SmCPS1</em> and inhibit its transcription. The results reveal the molecular mechanism of low-temperature regulation of tanshinone biosynthesis, which is of great significance for improving the post-harvest processing and quality enhancement of <em>S. miltiorrhiza</em>.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113058"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146220888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fine mapping of the qSCT12 locus conferring seedling cold tolerance in Oryza nivara","authors":"Yanju Zhu ,&nbsp;Qile Sun ,&nbsp;Shanshan Wang ,&nbsp;Fengxia Liu","doi":"10.1016/j.plantsci.2026.113070","DOIUrl":"10.1016/j.plantsci.2026.113070","url":null,"abstract":"<div><div>Cold stress severely limits rice growth and yield, making it crucial to identify cold-tolerant QTLs and genes for effective molecular breeding. In this study, we detected four QTLs for seedling cold tolerance using the introgression lines derived from wild rice (<em>Oryza nivara</em>) and identified an introgression line Ra47 harboring the major QTL <em>qSCT12</em>, which exhibited a higher seedling survival rate under cold stress than its recipient parent 9311 (an elite <em>indica</em> cultivar). Using the F_2:3 population developed by backcrossing Ra47 with 9311, we confirmed the major QTL <em>qSCT12</em> for seedling cold tolerance, which explained up to 29.92% of the phenotypic variation in cold tolerance traits, and which allele from wild rice could enhance seedling cold tolerance. Using additional 2744 F₂ individuals, we narrowed the QTL <em>qSCT12</em> to a 21.8-kb region on chromosome 12 between markers CT321 and 3-F. This interval contains 2 candidate genes <em>LOC_Os12g10700</em> and <em>LOC_Os12g10710</em>. Further RNA-seq analysis of Ra47 and 9311 before and after cold treatment revealed that DEGs were enriched in primary metabolic process, cellular metabolic process, hydrolase activity and pyrophosphatase activity. These findings will provide important insights into the genetic basis of cold tolerance in rice seedlings and offer new genetic resources for developing cold-tolerant rice varieties.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"366 ","pages":"Article 113070"},"PeriodicalIF":4.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147326821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}