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Multiscale Emergence of Pre-Harvest Sprouting in Cereals: From Seed Dormancy to Field-Level Resilience. 谷物收获前发芽的多尺度出现:从种子休眠到田间恢复力。
IF 6.9 1区 生物学
Plant, Cell & Environment Pub Date : 2026-12-01 Epub Date: 2026-09-01 DOI: 10.1111/pce.70852
Deng-Ke Ma, Xiong Zhang, Wei Wang, A-Li Dai, Liu-Sheng Duan, Wei-Ming Tan
{"title":"Multiscale Emergence of Pre-Harvest Sprouting in Cereals: From Seed Dormancy to Field-Level Resilience.","authors":"Deng-Ke Ma, Xiong Zhang, Wei Wang, A-Li Dai, Liu-Sheng Duan, Wei-Ming Tan","doi":"10.1111/pce.70852","DOIUrl":"10.1111/pce.70852","url":null,"abstract":"<p><p>Pre-harvest sprouting (PHS) represents a major threat to global food security under increasingly variable climatic conditions. Current understanding is largely derived from controlled laboratory studies, whereas field PHS is a multi-scale phenomenon resulting from interactions among genetic regulation, spike and grain traits, heterogeneous environmental conditions, and agronomic management. Our knowledge of PHS mechanisms under field conditions remains limited, and a systematic, integrated control framework is still lacking. In this review, we synthesise advances in the genetic architecture, physiological regulation, phenotypic determinants, and environmental factors of PHS in cereals, with emphasis on integrating multi-scale regulatory networks with environmental drivers. We particularly focus on laboratory-field discrepancies and how environmental heterogeneity influences grain quality deterioration and PHS outcomes under field conditions., and further evaluate current control strategies for PHS, including breeding, agronomic management, and chemical regulation, especially their limitations, environmental dependence, and associated trade-offs in practical application. Finally, we propose that future PHS control will require integrating field-relevant phenotypes, genotype × environment × management interactions, multi-scale predictive modelling, and decision-support systems to improve field-level resilience to PHS under increasingly variable climatic conditions.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":"9770-9787"},"PeriodicalIF":6.9,"publicationDate":"2026-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148862849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The CsTBH-CsROP2 Module Regulates Waterlogging Tolerance via Auxin-Mediated Adventitious Root Formation in Cucumber. CsTBH-CsROP2模块通过生长素介导的不定根形成调控黄瓜耐涝能力。
IF 6.9 1区 生物学
Plant, Cell & Environment Pub Date : 2026-12-01 Epub Date: 2026-09-02 DOI: 10.1111/pce.70854
Lei Sun, Fang Wang, Mingming Dong, Xi Zhao, Yaqi Zhang, Li Shan, Sen Li, Shuai Yin, Xinyue Ma, Tiantian Pei, Yingqi Shi, Zhigang Tang, Shaozhen He, Xingwang Liu, Huazhong Ren
{"title":"The CsTBH-CsROP2 Module Regulates Waterlogging Tolerance via Auxin-Mediated Adventitious Root Formation in Cucumber.","authors":"Lei Sun, Fang Wang, Mingming Dong, Xi Zhao, Yaqi Zhang, Li Shan, Sen Li, Shuai Yin, Xinyue Ma, Tiantian Pei, Yingqi Shi, Zhigang Tang, Shaozhen He, Xingwang Liu, Huazhong Ren","doi":"10.1111/pce.70854","DOIUrl":"10.1111/pce.70854","url":null,"abstract":"<p><p>Cucumber (Cucumis sativus L.) requires frequent irrigation due to its shallow root system and high transpiration rate of the aboveground parts. However, it is also prone to waterlogging damage. Therefore, understanding its response to waterlogging is crucial for breeding waterlogging-tolerant varieties. Although Rho of Plants GTPases play well-established roles in regulating development and stress signalling, their functions in plant adaptation to waterlogging stress has yet to be fully elucidated. Here, we identified nine CsROP genes in the cucumber genome, which exhibit evolutionary diversification but retain conserved functional domains. Functional analysis revealed that CsROP2 acts as a negative regulator of adventitious root formation. It modulates auxin accumulation in hypocotyl vascular bundles, thereby suppressing adventitious root development and enhancing waterlogging sensitivity. The HD-Zip I transcription factor CsTBH directly binds the CsROP2 promoter and activates its expression. Our study uncovers a CsTBH-CsROP2 module that governs adventitious rooting and waterlogging tolerance by modulating auxin homeostasis. These findings provide new insights into the crosstalk between developmental programmes and stress signalling pathways and offer potential genetic targets for improving stress resilience in cucumber and other crops.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":"9947-9969"},"PeriodicalIF":6.9,"publicationDate":"2026-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148878582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The SlJAZ2/SlJAZ3 Dimer Acts as a Switch of the SlMYC2-SlPR2 Module to Regulate the Cf-19-Mediated Resistance of Tomatoes to Cladosporium fulvum. SlJAZ2/SlJAZ3二聚体作为SlMYC2-SlPR2模块的开关调控cf -19介导的番茄对黄枝孢杆菌抗性
IF 6.9 1区 生物学
Plant, Cell & Environment Pub Date : 2026-12-01 Epub Date: 2026-09-11 DOI: 10.1111/pce.70873
Tong Pei, Xueli Jia, He Zhang, Dalong Li, Xiangyang Xu, Tingting Zhao
{"title":"The SlJAZ2/SlJAZ3 Dimer Acts as a Switch of the SlMYC2-SlPR2 Module to Regulate the Cf-19-Mediated Resistance of Tomatoes to Cladosporium fulvum.","authors":"Tong Pei, Xueli Jia, He Zhang, Dalong Li, Xiangyang Xu, Tingting Zhao","doi":"10.1111/pce.70873","DOIUrl":"10.1111/pce.70873","url":null,"abstract":"<p><p>Tomato leaf mold caused by Cladosporium fulvum (C. fulvum) is a devastating disease in tomato cultivation and production. The Cf gene confers resistance to C. fulvum. In our previous study, several JAZ family genes were found to be differentially expressed between resistant (Cf-19-mediated) and susceptible materials, especially SlJAZ3, whose expression was significantly upregulated during the Cf-19-mediated resistance response process. To explore the regulatory function of JAZ genes in this disease resistance system, this study focused on SlJAZ3 and found that both SlJAZ3 and its interacting protein SlJAZ2 can positively regulate the resistance response mediated by Cf-19. In addition, SlMYC2, as a positive regulator of the resistance response, can interact with SlJAZ2 (or SlJAZ3) and activate the expression of SlPR2. Notably, SlJAZ3 (or SlJAZ2) competitively binds to SlJAZ2 (or SlJAZ3), reducing its binding to SlMYC2, which helps to restore the transcriptional activation of the downstream defense gene SlPR2. Our findings reveal that the SlJAZ2/SlJAZ3 dimer regulates downstream signal transduction. This study has improved our understanding of Cf-mediated resistance and plant immune mechanisms, laying the foundation for the molecular improvement of tomato disease resistance and endows new significance to the formation of the JAZ-JAZ dimer.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":"10133-10148"},"PeriodicalIF":6.9,"publicationDate":"2026-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148928538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
CCRG1 Bridges Circadian Clock Regulation to Plant Developmental Transitions via Ubiquitin-Mediated Control. CCRG1通过泛素介导的调控在植物发育转变的生物钟调节中起桥梁作用。
IF 6.9 1区 生物学
Plant, Cell & Environment Pub Date : 2026-12-01 Epub Date: 2026-09-22 DOI: 10.1111/pce.70918
Ran Chu, Jialin Wang, Zhen Wei
{"title":"CCRG1 Bridges Circadian Clock Regulation to Plant Developmental Transitions via Ubiquitin-Mediated Control.","authors":"Ran Chu, Jialin Wang, Zhen Wei","doi":"10.1111/pce.70918","DOIUrl":"10.1111/pce.70918","url":null,"abstract":"","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":"10502-10504"},"PeriodicalIF":6.9,"publicationDate":"2026-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149023532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Pollen Carbonic Anhydrase Promotes Male Fertility Under Elevated Carbon Dioxide in Tomato. 一种花粉碳酸酐酶在高二氧化碳条件下促进番茄雄性育性。
IF 6.9 1区 生物学
Plant, Cell & Environment Pub Date : 2026-12-01 Epub Date: 2026-09-23 DOI: 10.1111/pce.70919
Jianrong Lv, Haiming Ying, Chenxin Yue, Zhengran Zhao, Shurong Wu, Rui Deng, Wenshan Zai, Cunnian Fu, Huan Liu, Christine H Foyer, Kai Shi, Anran Wang
{"title":"A Pollen Carbonic Anhydrase Promotes Male Fertility Under Elevated Carbon Dioxide in Tomato.","authors":"Jianrong Lv, Haiming Ying, Chenxin Yue, Zhengran Zhao, Shurong Wu, Rui Deng, Wenshan Zai, Cunnian Fu, Huan Liu, Christine H Foyer, Kai Shi, Anran Wang","doi":"10.1111/pce.70919","DOIUrl":"10.1111/pce.70919","url":null,"abstract":"<p><p>Rising atmospheric CO<sub>2</sub> is a defining feature of climate change and profoundly influences plant growth and productivity. While the effects of elevated CO<sub>2</sub> on photosynthesis and vegetative biomass have been extensively studied, its direct impact on male reproductive development remains poorly understood. Here, we show that elevated CO<sub>2</sub> improves pollen vigour and performance in tomato (Solanum lycopersicum). Through genetic and molecular analyses, we identify β-type carbonic anhydrase 2 (βCA2) as a pollen-enriched CO<sub>2</sub> sensor required for this response. Loss of βCA2 abolishes the promoting effects of elevated CO<sub>2</sub> on fertility, whereas βCA2 overexpression mimics the high-CO<sub>2</sub> phenotype under ambient conditions. Further analyses revealed that βCA2 regulates downstream networks involved in vesicle trafficking and intracellular transport to promote pollen germination, alongside cellulose and pectin metabolism required for pollen intine remodelling. These findings suggest a potential link between βCA2-mediated CO<sub>2</sub> perception, intracellular transport and pollen intine remodelling. Our results uncover a dynamic, pollen-specific CO<sub>2</sub> response pathway that integrates intracellular transport with structural wall remodelling, providing new insights into how plants sustain male fertility under rising atmospheric CO<sub>2</sub>.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":"10520-10532"},"PeriodicalIF":6.9,"publicationDate":"2026-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149029279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correction to "Complex Regulation of Retinoblastoma-Related's Interactions With E2Fs Via Phosphorylation". 更正“视网膜母细胞瘤相关的通过磷酸化与E2Fs相互作用的复杂调控”。
IF 6.9 1区 生物学
Plant, Cell & Environment Pub Date : 2026-12-01 Epub Date: 2026-10-06 DOI: 10.1111/pce.70949
{"title":"Correction to \"Complex Regulation of Retinoblastoma-Related's Interactions With E2Fs Via Phosphorylation\".","authors":"","doi":"10.1111/pce.70949","DOIUrl":"10.1111/pce.70949","url":null,"abstract":"","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":"10591"},"PeriodicalIF":6.9,"publicationDate":"2026-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149101621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
OsNCED5 Controls Abscisic Acid-Mediated Anther Dehiscence and Male Fertility in Rice. OsNCED5控制脱落酸介导的水稻花药开裂和雄性育性。
IF 6.9 1区 生物学
Plant, Cell & Environment Pub Date : 2026-12-01 Epub Date: 2026-08-30 DOI: 10.1111/pce.70842
Yi Chen, Min Liu, Zhipan Xiang, Shengping Wang, Lei Jin, Shufeng Gao, Yingyue Xia, Dan Cai, Tianze Yan, Qunfeng Zhou, Yanfeng Li, Yan Wu, Wanling Zhao, Gang Huang, Xiangrong Tian, Xiaojun Dai, Manzhong Liang, Jun Fu, Liangbi Chen, Dandan Mao
{"title":"OsNCED5 Controls Abscisic Acid-Mediated Anther Dehiscence and Male Fertility in Rice.","authors":"Yi Chen, Min Liu, Zhipan Xiang, Shengping Wang, Lei Jin, Shufeng Gao, Yingyue Xia, Dan Cai, Tianze Yan, Qunfeng Zhou, Yanfeng Li, Yan Wu, Wanling Zhao, Gang Huang, Xiangrong Tian, Xiaojun Dai, Manzhong Liang, Jun Fu, Liangbi Chen, Dandan Mao","doi":"10.1111/pce.70842","DOIUrl":"10.1111/pce.70842","url":null,"abstract":"<p><p>Proper anther dehiscence is essential for successful pollination and male fertility in flowering plants. However, many gaps remain in the regulatory mechanisms underlying anther dehiscence in plants, including a possible role for abscisic acid (ABA) in anther dehiscence. Here, we reported a member of 9-cis-epoxycarotenoid dioxygenase family (NCED), OsNCED5, which regulates proper anther dehiscence for male fertility in rice. OsNCED5 encodes a chloroplast-localized ABA biosynthetic enzyme highly expressed in anther during the late phase. Disruption of OsNCED5 by CRISPR/Cas9-mediated mutagenesis led to the reduction of ABA accumulation in anthers, thus the failure of secondary cell wall (SCW) thickening in anther endothecium due to loss of lignin biosynthesis, which eventually resulting in indehiscent anthers and significantly reduced fertility. Further analysis indicated that OsNCED5 probably confer a conserved fertility regulation mechanism between japonica and indica subspecies. Taken together, we have identified a key OsNCED regulator involved anther dehiscence -based male fertility, and provide a valuable genetic resource for fertility improvement in rice.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":"9715-9728"},"PeriodicalIF":6.9,"publicationDate":"2026-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148862831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rewiring the TaGSK3-TaGW2-Rht1 Module for Ideotype Wheat Varieties. 理想型小麦品种TaGSK3-TaGW2-Rht1模块的重新布线
IF 6.9 1区 生物学
Plant, Cell & Environment Pub Date : 2026-12-01 Epub Date: 2026-08-30 DOI: 10.1111/pce.70849
Yufan Wang, Yunwei Zhang, Shuxian Huang, Jiatong Qiu, Guozhong Sun, Jiaqiang Sun
{"title":"Rewiring the TaGSK3-TaGW2-Rht1 Module for Ideotype Wheat Varieties.","authors":"Yufan Wang, Yunwei Zhang, Shuxian Huang, Jiatong Qiu, Guozhong Sun, Jiaqiang Sun","doi":"10.1111/pce.70849","DOIUrl":"10.1111/pce.70849","url":null,"abstract":"","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":"9711-9714"},"PeriodicalIF":6.9,"publicationDate":"2026-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148862833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The OsSRLD-OsIMα1a-OsWRKY53 and OsSRLD-OsDIP1 Modules Balance Disease Resistance and Drought/Salt Tolerance in Rice. OsSRLD-OsIMα1a-OsWRKY53和OsSRLD-OsDIP1模块平衡水稻抗病性和抗旱性。
IF 6.9 1区 生物学
Plant, Cell & Environment Pub Date : 2026-12-01 Epub Date: 2026-08-31 DOI: 10.1111/pce.70856
Yapu Cheng, Kexing Fang, Tiancheng Qiu, Qingyuan Bai, Yayan Feng, Qingya Yang, Jun Yang, Xujun Chen, Vijai Bhadauria, You-Liang Peng, Wensheng Zhao
{"title":"The OsSRLD-OsIMα1a-OsWRKY53 and OsSRLD-OsDIP1 Modules Balance Disease Resistance and Drought/Salt Tolerance in Rice.","authors":"Yapu Cheng, Kexing Fang, Tiancheng Qiu, Qingyuan Bai, Yayan Feng, Qingya Yang, Jun Yang, Xujun Chen, Vijai Bhadauria, You-Liang Peng, Wensheng Zhao","doi":"10.1111/pce.70856","DOIUrl":"10.1111/pce.70856","url":null,"abstract":"<p><p>Understanding the molecular mechanisms underlying plant responses to various stresses is crucial for improving crop productivity under stressful conditions. However, how plants prioritize the activation of pathways to balance disease resistance with drought and salt tolerance remains unclear. Here, we identify two regulatory modules centered on the rice protein OsSRLD, which negatively regulates disease resistance and positively regulates drought/salt tolerance. Upregulation of OsSRLD increases ABA content and reduces ROS levels under both normal and stressed conditions, suggesting its involvement in ABA signaling and ROS homeostasis. As an E3 ligase, OsSRLD interacts with OsIMα1a (a positive regulator of disease resistance) and promotes its ubiquitination and degradation via the 26S proteasome. Additionally, OsIMα1a interacts with OsWRKY53 (a positive regulator of disease resistance but a negative regulator of salt tolerance), thereby promoting the nuclear accumulation of OsWRKY53. Consistently, both overexpression of OsSRLD and knockout of OsIMα1a resulted in downregulation of OsWRKY53-activated genes and upregulation of OsWRKY53-inactivated genes. Furthermore, OsSRLD interacts with and stabilizes OsDIP1 (a positive regulator of drought and salt tolerance) via an E3 ligase-independent pathway. Together, our findings reveal that OsSRLD-OsIMα1a-OsWRKY53 and OsSRLD-OsDIP1 modules balance disease resistance and drought/salt tolerance through both E3 ligase-dependent and E3 ligase-independent pathways.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":"9788-9807"},"PeriodicalIF":6.9,"publicationDate":"2026-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148862940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Integrative Multi-Omics Analysis of Stem Growth Habit Divergence in Wild Soybean (Glycine soja). 野生大豆(甘氨酸大豆)茎生长习性差异的多组学综合分析。
IF 6.9 1区 生物学
Plant, Cell & Environment Pub Date : 2026-12-01 Epub Date: 2026-09-10 DOI: 10.1111/pce.70872
Xiulin Liu, Xueyang Wang, Huilong Hong, Kenzhen Zhao, Chunlei Zhang, Fengyi Zhang, Rongqiang Yuan, Dai Shi, Sobhi F Lamlom, Bixian Zhang, Honglei Ren
{"title":"Integrative Multi-Omics Analysis of Stem Growth Habit Divergence in Wild Soybean (Glycine soja).","authors":"Xiulin Liu, Xueyang Wang, Huilong Hong, Kenzhen Zhao, Chunlei Zhang, Fengyi Zhang, Rongqiang Yuan, Dai Shi, Sobhi F Lamlom, Bixian Zhang, Honglei Ren","doi":"10.1111/pce.70872","DOIUrl":"10.1111/pce.70872","url":null,"abstract":"<p><p>Stem architecture is a major determinant of lodging resistance, biomass accumulation, and harvest efficiency in soybean. However, the molecular features associated with contrasting stem growth habits in wild soybean remain incompletely characterised. Here, we performed an integrated transcriptomic, metabolomic, and epigenomic analysis of stem growth-habit divergence in wild soybean, comparing the wild-type accession ZYD7068 with contrasting vining and erect mutant lines derived from carbon-ion beam mutagenesis. Pairwise transcriptomic comparisons identified between 20 311 and 28 705 differentially expressed genes per contrast, with a core set of 2672 genes consistently altered across the comparisons. Functional enrichment, gene set variation analysis, and gene set enrichment analysis converged on xylem and phloem pattern formation as a prominent molecular pathway associated with growth-habit divergence. Random forest analysis identified BBR-BPC and ARF transcription factor families as major molecular discriminators, while metabolomic profiling revealed distinct metabolic profiles involving amino-acid-derived and lipid-associated metabolites. Whole-genome bisulfite sequencing revealed context-specific DNA methylation differences, including substantial variation in CHG methylation among erect mutant lines. Integrated network and in silico perturbation analyses prioritised four candidate genes associated with vascular development for future functional validation. Together, these results provide a multi-layer molecular resource for investigating stem growth-habit divergence in G. soja and establish testable candidate pathways and genes for subsequent functional studies and soybean improvement.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":"10064-10080"},"PeriodicalIF":6.9,"publicationDate":"2026-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148917609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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