The Plant Journal最新文献

{"title":"OsYchF1 suppresses OsEF1Bγ-mediated ER detoxification to co-involve the growth-maintenance trade-off in rice","authors":"Liyang Gao,&nbsp;Lulu Yu,&nbsp;Dongyu Chen,&nbsp;Rongfang Li,&nbsp;Yuhe Wang,&nbsp;Yunchuan Liao,&nbsp;Yetao Meng,&nbsp;Qian Li,&nbsp;Ying Miao,&nbsp;Gefei Hao,&nbsp;Rui Miao","doi":"10.1111/tpj.71185","DOIUrl":"10.1111/tpj.71185","url":null,"abstract":"<p>Translation elongation is a fundamental biological process, yet its direct role in stress adaptation remains unclear. In this study, we uncover a novel regulatory axis in rice involving the unconventional G protein OsYchF1, which gates the detoxification activity of the elongation factor 1Bγ (OsEF1Bγ) in the endoplasmic reticulum. OsEF1Bγ is a subunit of the eEF1B complex and possesses an N-terminal glutathione S-transferase (GST) domain. We demonstrate that overexpression of OsEF1Bγ enhances rice tolerance to osmotic and saline stress by lowering malondialdehyde levels, suggesting its role as a positive regulator <i>via</i> GST-mediated detoxification. Conversely, we found that OsYchF1 interacts with OsEF1Bγ across multiple domains. This interaction competitively inhibits the binding of reduced glutathione to OsEF1Bγ by approximately 40-fold, thereby suppressing its GST activity <i>in vitro</i>. Consistently, <i>OsYchF1</i> knockout mutants phenocopy OsEF1Bγ overexpressors, displaying enhanced stress tolerance, reduced reactive oxygen species accumulation, and increased antioxidant enzyme activities. Furthermore, we show that stress-induced downregulation of OsYchF1 acts as a physiological trigger, releasing this molecular brake to enable rapid activation of OsEF1Bγ-mediated detoxification in response to challenging environments. Collectively, our findings reveal a post-translational mechanism where OsYchF1 serves as a molecular brake on the ER-localized detoxification engine of OsEF1Bγ, fine-tuning abiotic stress adaptation and establishing an unexpected link between the translation machinery and cellular redox homeostasis.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 3","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71185","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149293696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Natural variation in the evolutionarily conserved F-box gene SDEF promotes seed dormancy in rice","authors":"Yuliang Zhou,&nbsp;Yueping Wang,&nbsp;Guangmiao Zhao,&nbsp;Chunbao Liu,&nbsp;Ruizhen Zeng,&nbsp;Wenxuan Liang,&nbsp;Ru Han,&nbsp;Hui Kong,&nbsp;Xiaofan Cao,&nbsp;Minshi Li,&nbsp;Huhui Chen,&nbsp;Bin Tan,&nbsp;Hong Liu,&nbsp;Zhenjiang Xu","doi":"10.1111/tpj.71203","DOIUrl":"10.1111/tpj.71203","url":null,"abstract":"<p>Insufficient seed dormancy causes pre-harvest sprouting (PHS) and severe yield losses in rice; however, genetic resources with practical breeding value remain limited. Here, we isolated a major dormancy gene, <i>SDEF</i>, via map-based cloning using chromosomal single segment substitution lines (SSSLs), identifying a functional SNP (Arg-to-Trp) as the causal mutation. CRISPR/Cas9-mediated knockout of <i>SDEF</i> led to PHS susceptibility, while overexpression significantly enhanced dormancy. Importantly, <i>SDEF</i> enhanced seed dormancy without compromising grain yield in SSSLs, confirming it as a promising breeding target. Moreover, <i>SDEF</i> encodes an angiosperm-conserved, nuclear-localized F-box protein and is preferentially expressed in the embryo, with expression increasing during seed maturation and declining upon germination. Mechanistically, protein interaction assays confirmed that SDEF recruits OSK1, with the Trp-type SDEF^K exhibiting a more stable interaction than the Arg-type SDEF^H. <i>SDEF</i> is induced by abscisic acid (ABA) and appears to promote seed dormancy through the ABA pathway by activating ABA signaling genes and repressing α-amylase genes, as evidenced by the reduced ABA sensitivity of <i>sdef</i> mutants. Additionally, haplotype analysis revealed that natural variation in <i>SDEF</i> is associated with divergent dormancy levels, and reduced nucleotide diversity in cultivated rice indicates that <i>SDEF</i> was selected during domestication. Collectively, our results provide insights into the molecular basis of <i>SDEF-</i>mediated dormancy, providing an ideal target for breeding PHS-resistant rice.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 3","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71203","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149293717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to “GT1 regulates maize sex determination by affecting the jasmonate pathway”","authors":"","doi":"10.1111/tpj.71193","DOIUrl":"10.1111/tpj.71193","url":null,"abstract":"<p>\u0000 <span>Lin, Z.</span>, <span>Yang, J.</span>, <span>Liu, S.</span>, <span>Bai, Y.</span>, <span>Li, W.</span>, <span>Lai, J.</span>, et al. (<span>2025</span>) <span><i>GT1</i> regulates maize sex determination by affecting the jasmonate pathway</span>. <i>The Plant Journal</i>, <span>123</span>, e70306. Available from: https://doi.org/10.1111/tpj.70306\u0000 </p><p>In the Results section, second paragraph, under the heading ‘<i>GT1</i> regulates maize sex determination by directly modulating JA biosynthesis’, the phrase ‘the primary active forms of JA’ should instead read ‘the primary forms of JA’. The word ‘active’ has been removed.</p><p>These corrections do not alter the original data, statistical analyses, or the conclusions of the article.</p><p>We apologize for these errors.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13717935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149293749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sorghum Metabolic Atlas: A fluorescent protein-based subcellular localization resource for sorghum enzymes","authors":"Purva Karia,&nbsp;William P. Dwyer,&nbsp;Ava Kloss-Schmidt,&nbsp;Charles Hawkins,&nbsp;Bo Xue,&nbsp;Daniel Ginzburg,&nbsp;Maxine L. Gutierrez,&nbsp;Ritesh Mewalal,&nbsp;Ian Blaby,&nbsp;David W. Ehrhardt,&nbsp;Seung Y. Rhee","doi":"10.1111/tpj.71166","DOIUrl":"10.1111/tpj.71166","url":null,"abstract":"<p>Plant metabolism drives traits essential for productivity and resilience, yet understanding metabolic networks requires subcellular, cellular, and tissue-level spatial context that remains limited, particularly in crop species. Experimentally derived subcellular localization data for enzymes are sparse, constraining analyses of metabolic organization in the cell. We developed a high-throughput protoplast transformation and fluorescent protein (FP) tagging system optimized for <i>Sorghum bicolor</i>, a climate-resilient C₄ crop. Using this platform, we experimentally determined the subcellular localization of 234 metabolic enzymes spanning 184 pathways. The sorghum enzymes we characterized localize to 12 subcellular compartments. Comparison with computational predictions highlights variable accuracy across compartments, and cross-species comparison with <i>Arabidopsis thaliana</i> shows partial agreement with available experimental data. All data are accessible through the Sorghum Metabolic Atlas (www.sorghummetabolicatlas.org) web platform, enabling search, visualization, and download. This study presents a large-scale experimental dataset of enzyme localization in sorghum, providing a resource for studies of plant metabolic organization and comparative analyses.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 3","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71166","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149293733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nuclear importin α1 AtIMPA1 regulates stomatal reopening to defend against Pst DC3000 by orchestrating ABA signaling","authors":"Ting Zhang,&nbsp;Kang Wang,&nbsp;Yi Guan,&nbsp;Jingao Zhang,&nbsp;Charles Tetteh,&nbsp;Chenxi Liu,&nbsp;Cheng Zhang,&nbsp;Pinyuan Jin,&nbsp;Sheng Luo,&nbsp;Yiling Wang,&nbsp;Huajian Zhang","doi":"10.1111/tpj.71175","DOIUrl":"10.1111/tpj.71175","url":null,"abstract":"<p>Importin α family proteins serve as essential carriers for transporting specific disease-resistant proteins into the nucleus, enabling these proteins to function properly. However, whether importin α proteins are involved in plant immunity remains unclear. Here, we characterized a guard cell-expressed protein importin α1 AtIMPA1, which contributed to resistance against <i>Pseudomonas syringae</i> pv. <i>tomato</i> DC3000 (<i>Pst</i> DC3000). When dip-inoculated with <i>Pst</i> DC3000, the <i>impa1</i> mutants exhibited increased susceptibility, along with significant stomatal reopening induced by the phytotoxin coronatine (COR) secreted by <i>Pst</i> DC3000; while overexpression of <i>AtIMPA1</i> enhanced resistance to <i>Pst</i> DC3000 with compromised stomatal reopening induced by COR. Notably, following syringe-infiltration of <i>Pst</i> DC3000, the <i>impa1</i> mutants showed increased resistance, whereas overexpression lines were more susceptible to <i>Pst</i> DC3000, indicating that COR-triggered stomatal reopening is a primary determinant in AtIMPA1-mediated disease resistance. Further investigations revealed that AtIMPA1 regulated COR-triggered stomatal reopening is linked to abscisic acid (ABA) signaling. Mutation of <i>AtIMPA1</i> attenuated the ABA-mediated inhibition of root length and seed germination, and disrupted the ABA-induced protein abundance and localization of the ABA-responsive protein, supporting its role in regulating the ABA response. These findings shed light on the functional significance of AtIMPA1 in COR-triggered stomatal reopening and provided new insights into how importin α proteins orchestrate ABA signaling to regulate plant immunity.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 3","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71175","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149293675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the molecular basis of maize cold tolerance via integrative regulatory network analysis","authors":"Tianshuo Li,&nbsp;Wei Wang,&nbsp;Chuang Jiang,&nbsp;Jinkui Cheng,&nbsp;Fei Yi,&nbsp;Liusheng Duan","doi":"10.1111/tpj.71197","DOIUrl":"10.1111/tpj.71197","url":null,"abstract":"<p>Maize (<i>Zea mays</i> L.) is a globally critical but cold-sensitive crop. Understanding the temporal organization of cold-responsive, circadian-associated, and hormone-associated transcriptional programs is essential for deciphering how plants balance growth and survival under cold stress to ensure food security. We performed high-resolution time-series RNA-seq on 108 maize seedling samples across 14 time points (0–36 h cold stress and 24 h recovery). Coronatine (COR) was utilized as a defined JA-associated chemical perturbation to probe hormone-associated transcriptional responses during cold stress. We identified 12 986 cold-responsive and 2259 recovery-responsive genes, revealing a recovery-associated transcriptional transition characterized by suppressed photosynthesis-related processes and enrichment of genes associated with lipid catabolism, accompanied by transient physiological stress during early recovery. Cold stress induced widespread phase shifts and reduced oscillation amplitudes among circadian-associated transcripts, while COR identified distinct hormone-associated transcriptional modules and candidate network-associated genes, including <i>ZmWRKY71</i> and <i>ZmHSP28</i>, whose roles were further supported by molecular and genetic analyses. This study establishes a temporally resolved transcriptional framework for maize cold stress and recovery, integrating transcriptional dynamics, physiological responses, and experimentally supported regulatory nodes.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 3","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71197","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149293700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lessons from the past: resurrecting an ancestral strigolactone receptor","authors":"Brian C. Mooney","doi":"10.1111/tpj.71189","DOIUrl":"10.1111/tpj.71189","url":null,"abstract":"&lt;p&gt;Plants use an array of phytohormones to coordinate their growth and communicate with the organisms around them. Strigolactones (SLs) are a class of butenolide phytohormones with a wide range of physiological roles. First identified as root exudates that could stimulate the germination of parasitic &lt;i&gt;Striga&lt;/i&gt; plants, they were later found to promote symbioses with arbuscular mycorrhizal fungi and root bacteria. Within the plant, SLs regulate several aspects of development, most notably by suppressing shoot branching (Kelly et al., &lt;span&gt;2023&lt;/span&gt;).&lt;/p&gt;&lt;p&gt;In seed plants, SLs are perceived by DWARF14 (D14), which acts as both a receptor and an α/β-hydrolase enzyme. D14 binds SLs within a hydrophobic pocket and hydrolyses them using a catalytic triad of serine, aspartate and histidine residues. Ligand perception also triggers a conformational change that enables D14 to interact with the F-box protein MORE AXILLARY GROWTH 2 (MAX2), leading to the degradation of SUPPRESSOR OF MAX2-LIKE/DWARF 53 (SMXL/D53) transcriptional repressors and induction of SL-responsive genes. Intriguingly, however, the relationship between the enzymatic and signalling functions of D14 remains unresolved. Mutating its catalytic aspartate abolishes SL hydrolysis without preventing signalling in &lt;i&gt;Arabidopsis&lt;/i&gt;, suggesting that ligand binding, rather than hydrolysis, is sufficient to activate the receptor (Seto et al., &lt;span&gt;2019&lt;/span&gt;).&lt;/p&gt;&lt;p&gt;D14 belongs to a larger family of related α/β-hydrolases that includes KARRIKIN INSENSITIVE 2 (KAI2). KAI2 is a receptor for karrikins, plant growth regulators that structurally resemble SLs and are found in the smoke from burning plants. KAI2 homologues are found throughout land plants and algae, whereas D14 is restricted to seed plants, suggesting that D14 evolved following duplication and neofunctionalisation of an ancestral KAI2-like protein. Although modern KAI2 and D14 proteins share structural and mechanistic similarities, they have distinct ligand preferences and cannot substitute for one another in &lt;i&gt;Arabidopsis&lt;/i&gt;. How and when D14 acquired the characteristics of a specialised SL receptor thus remains an intriguing evolutionary question.&lt;/p&gt;&lt;p&gt;Associate Professor Mark Waters at The University of Western Australia first became interested in SL perception through his group's work on karrikins. In particular, the group was curious about the evolutionary changes that led to the distinct activities of KAI2 and D14. Waters wondered whether an early D14 present at the origin of seed plants might retain KAI2-like characteristics, potentially revealing an intermediate stage in the transition from ancestor to a modern SL receptor. In their new study, Waters and colleagues travelled back along this evolutionary trajectory using ancestral sequence reconstruction (ASR) (Tuckey et al., &lt;span&gt;2026&lt;/span&gt;). ASR uses phylogenetic relationships between modern proteins to infer sequences that may have existed in their common ancestors","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13717938/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149293738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell transcriptome atlas reveals a WRKY33-HSP81 regulatory module that orchestrates phenylpropanoid-mediated defense against Sclerotium rolfsii in Dendrobium officinale","authors":"Lingli Li,&nbsp;Ye Xu,&nbsp;Wei Liu,&nbsp;Zhitao Niu,&nbsp;Qingyun Xue,&nbsp;Xiaoyu Ding","doi":"10.1111/tpj.71190","DOIUrl":"10.1111/tpj.71190","url":null,"abstract":"<p>Plants employ cell-type-specific transcriptional programs to defend against pathogens, yet the cellular heterogeneity of immune responses in the medicinal orchid <i>Dendrobium officinale</i> Kimura et Migo remains largely unexplored. A single-cell transcriptomic atlas of the <i>D. officinale</i> stem base upon <i>Sclerotium rolfsii</i> infection was constructed, profiling over 20 000 cells across 12 and 24 h post-infection. A total of 21 cell clusters were resolved into 6 major cell types—epidermal, ground tissue parenchyma, proliferating, xylem, phloem, and vascular bundle parenchyma cells—with identities validated by fluorescence <i>in situ</i> hybridization. Cell-type-specific analyses revealed that epidermal and phloem cells mounted early defense responses, while xylem cells exhibited the most extensive transcriptional reprogramming at 24 hpi, coinciding with the activation of lignin biosynthesis pathways. <i>WRKY33</i> was identified as a central transcriptional activator that directly binds W-box motifs in the promoters of lignin biosynthetic genes <i>C4H</i> and <i>HCT</i>, promoting lignin deposition and enhancing disease resistance. Conversely, the nuclear-localized chaperone <i>HSP81</i> physically interacts with <i>WRKY33</i> and functions as a broad regulator of multiple transcription factors via co-factor sequestration, thereby compromising defense when overexpressed. These findings uncover a <i>WRKY33</i>-<i>HSP81</i> regulatory module that orchestrates phenylpropanoid-mediated defense in <i>D. officinale</i>, providing a high-resolution cellular framework for understanding plant immunity and offering potential targets for improving disease resistance in this economically valuable species.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 3","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71190","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149293725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An efficient gene delivery method utilizing the regenerative capacity of alfalfa (Medicago sativa)","authors":"Jinghui Gao,&nbsp;Houyin Xia,&nbsp;Yajun Wu,&nbsp;Changgen Xie,&nbsp;Jiawen Peng,&nbsp;Yilin Cui,&nbsp;Yiyang Liu,&nbsp;Luna Tan,&nbsp;Chun Li,&nbsp;Qian Li,&nbsp;Jie An,&nbsp;Peizhi Yang","doi":"10.1111/tpj.71195","DOIUrl":"10.1111/tpj.71195","url":null,"abstract":"<p>Alfalfa (<i>Medicago sativa</i>), an autotetraploid species, is a globally important forage crop. Traditional genetic transformation methods predominantly rely on leaf-derived callus, a process that is complex, inefficient, and particularly challenging to generate stable transgenic lines in polyploid plants. To address these limitations, we developed an efficient transformation system that bypasses callus induction by directly exploiting stem regeneration. Our protocol enables the generation of stable gene-edited alfalfa plants from shoot tips. It accommodates stem explants from various developmental stages and significantly reduces the time required. Moreover, this approach was effective across multiple alfalfa cultivars, and preliminary proof-of-concept experiments in <i>Nicotiana tabacum</i> and <i>Solanum lycopersicum</i> suggested potential transferability beyond alfalfa. This study represents a substantial advancement in perennial plant transformation and provides a robust and practical platform for optimizing stem regeneration-based genetic modification systems.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 3","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71195","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149293746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic architecture of low-temperature germinability in rice revealed by integrated maps of SNPs and structural variation","authors":"Youshuai Shi,&nbsp;Kai Xu,&nbsp;Yamei Lv,&nbsp;Xiaoyu He,&nbsp;Tingting Yu,&nbsp;Fengcai Wu,&nbsp;Lunping Liang,&nbsp;Ting Feng,&nbsp;Liang Zhang,&nbsp;Erbao Liu,&nbsp;Zhikang Li,&nbsp;Wensheng Wang,&nbsp;Min Li,&nbsp;Chaopu Zhang","doi":"10.1111/tpj.71184","DOIUrl":"https://doi.org/10.1111/tpj.71184","url":null,"abstract":"<p>Low-temperature germinability (LTG) limits rice direct seeding, yet its genetic architecture and regulatory roles of structural variations (SVs) remain largely unclear. We evaluated LTG in 403 rice accessions at four temperatures (13°C, 15°C, 18°C, 21°C). Integrating SNP/SV–GWAS, RNA-seq, gene editing, population genetics, and machine learning, we dissected the genetic basis of LTG and built a genomic selection (GS) prediction model. The panel showed extensive LTG variation, which was negatively correlated with origin latitude. SV- and SNP-based GWAS for LTG detected 119 and 127 QTLs, respectively, with 25 loci overlapping between the two datasets. Combining GWAS and RNA-seq, we screened 30 candidate genes and 48 favorable haplotypes, with high-LTG favorable alleles enriched in low-latitude <i>Xian</i> (<i>Indica</i>) accessions. We identified a deletion in the <i>qLTG3-1</i> coding region that negatively regulated LTG, and gene editing (CRISPR/Cas9) confirmed <i>qLT11d</i> is a key gene for LTG. Population genetic analysis identified 29 inter-subspecies (<i>Xian–Geng</i>) and 37 intra-<i>Xian</i> divergent regions for LTG, implying shared selected regions across and within subspecies under low temperature. Using SNP and SV data, we built corresponding genomic selection (GS) models with the machine learning-based MFGP method, achieving high prediction accuracy across all temperatures. All cross-temperature prediction correlations exceeded 0.55, with optimal performance at 18°C. Our results clarify rice LTG genetic architecture and suggest potential regulatory roles for SVs that merit further investigation, providing candidate genes, favorable haplotypes, and a GS model for LTG genetic improvement in direct seeding rice.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"128 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.71184","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149259412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}