Circular RNAs (circRNAs) play important roles in plant stress responses, yet their dynamic regulation during stress remains unclear. This study elucidates a molecular mechanism whereby the grapevine U2 snRNP core component VvU2A' enhances salt tolerance through a circRNA-mediated post-transcriptional network. We found that VvU2A' expression is induced by salt stress and positively regulates salt tolerance in grapevine. CircRNA sequencing revealed 497 VvU2A'-regulated differentially expressed circRNAs, including downregulated VvcircHMA1. Mechanistic investigation revealed that VvcircHMA1 acts as a competitive endogenous RNA (ceRNA) by sequestering VvmiR167b, thereby attenuating its cleavage activity on the target mRNA VvARF6. Functional analyses revealed that both VvcircHMA1 and VvARF6 negatively regulate salt tolerance, while VvmiR167b positively regulates it. Collectively, our study reveals a novel mechanism by which the splicing factor VvU2A' enhances salt stress response through the VvcircHMA1-VvmiR167b-VvARF6 cascade, providing promising molecular targets for breeding salt-resistant grapevines.
{"title":"VvU2A' -mediated circRNA biogenesis confers salt tolerance in grapevine via the VvcircHMA1 -VvmiR167b- VvARF6 pathway","authors":"Zhen Gao, Le Zheng, Yeqi Li, Jing Li, Yuanpeng Du","doi":"10.1093/hr/uhaf355","DOIUrl":"https://doi.org/10.1093/hr/uhaf355","url":null,"abstract":"Circular RNAs (circRNAs) play important roles in plant stress responses, yet their dynamic regulation during stress remains unclear. This study elucidates a molecular mechanism whereby the grapevine U2 snRNP core component VvU2A' enhances salt tolerance through a circRNA-mediated post-transcriptional network. We found that VvU2A' expression is induced by salt stress and positively regulates salt tolerance in grapevine. CircRNA sequencing revealed 497 VvU2A'-regulated differentially expressed circRNAs, including downregulated VvcircHMA1. Mechanistic investigation revealed that VvcircHMA1 acts as a competitive endogenous RNA (ceRNA) by sequestering VvmiR167b, thereby attenuating its cleavage activity on the target mRNA VvARF6. Functional analyses revealed that both VvcircHMA1 and VvARF6 negatively regulate salt tolerance, while VvmiR167b positively regulates it. Collectively, our study reveals a novel mechanism by which the splicing factor VvU2A' enhances salt stress response through the VvcircHMA1-VvmiR167b-VvARF6 cascade, providing promising molecular targets for breeding salt-resistant grapevines.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"1 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145801223","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}
The shikimate pathway is critical for the biosynthesis of aromatic amino acids and a diverse array of secondary metabolites in plants, including anthocyanins. Erythrose-4-phosphate (E4P) serves as a crucial precursor in the shikimate pathway. Transaldolase (TA) and transketolase (TK) are two pivotal enzymes involved in E4P synthesis in plants through the oxidative pentose phosphate pathway (OPPP) and Calvin cycle pathways. During the coloring stage of flowers, a large number of anthocyanins accumulate. However, the source of E4P required for anthocyanin accumulation is still unknown. In this study, we characterized the TA and TK family members in petunia (Petunia hybrida), an important ornamental plant. Virus-induced gene silencing (VIGS) and RNAi techniques indicated that PhTA1 or PhTA2 silencing did not lead to visible phenotype change in petunia, while cosilencing of PhTK1-TK2 resulted in significantly lighter colors in flowers and leaves. The levels of anthocyanins, chlorophyll, E4P, flavonoids, and three aromatic amino acids all significantly decreased in PhTK1-TK2-silenced plants compared with the control. Additionally, cosilencing of PhTK1 and PhTK2 disrupted the flavonoid metabolome profile in petunia flowers. In summary, PhTK1 and PhTK2 provide the primary E4P source for anthocyanin biosynthesis.
{"title":"Transketolase-mediated erythrose-4-phosphate provides an essential source for anthocyanin biosynthesis in petunia.","authors":"Xin Li,Wenjie Yang,Jiahao Cao,Wenqi Deng,Chenxi Wang,Yi Yao,Weiyuan Yang,Yixun Yu,Shiwei Zhong,Juanxu Liu","doi":"10.1093/hr/uhaf285","DOIUrl":"https://doi.org/10.1093/hr/uhaf285","url":null,"abstract":"The shikimate pathway is critical for the biosynthesis of aromatic amino acids and a diverse array of secondary metabolites in plants, including anthocyanins. Erythrose-4-phosphate (E4P) serves as a crucial precursor in the shikimate pathway. Transaldolase (TA) and transketolase (TK) are two pivotal enzymes involved in E4P synthesis in plants through the oxidative pentose phosphate pathway (OPPP) and Calvin cycle pathways. During the coloring stage of flowers, a large number of anthocyanins accumulate. However, the source of E4P required for anthocyanin accumulation is still unknown. In this study, we characterized the TA and TK family members in petunia (Petunia hybrida), an important ornamental plant. Virus-induced gene silencing (VIGS) and RNAi techniques indicated that PhTA1 or PhTA2 silencing did not lead to visible phenotype change in petunia, while cosilencing of PhTK1-TK2 resulted in significantly lighter colors in flowers and leaves. The levels of anthocyanins, chlorophyll, E4P, flavonoids, and three aromatic amino acids all significantly decreased in PhTK1-TK2-silenced plants compared with the control. Additionally, cosilencing of PhTK1 and PhTK2 disrupted the flavonoid metabolome profile in petunia flowers. In summary, PhTK1 and PhTK2 provide the primary E4P source for anthocyanin biosynthesis.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"2 1","pages":"uhaf285"},"PeriodicalIF":8.7,"publicationDate":"2025-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145813559","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}
The female flower gives rise to the fruit/seed and thus directly affects crop yield in unisexual plants. Both ethylene and auxin promote femaleness in cucurbits. However, how auxin regulates sex determination has been an open question over half a century. The recent publication (Han et al., Science, 2025) identified auxin response factor CsARF3 as a crucial player in auxin-promoting femaleness, and revealed a reciprocal relationship between auxin and ethylene during female flower determination.
在单性植物中，雌花产生果实/种子，从而直接影响作物产量。乙烯和生长素都能促进葫芦的雌性化。然而，半个多世纪以来，生长素如何调节性别决定一直是一个悬而未决的问题。最近发表的论文（Han et al., Science, 2025）发现生长素反应因子CsARF3在生长素促进雌性的过程中起着至关重要的作用，并揭示了生长素和乙烯在雌花决定过程中的相互关系。
{"title":"Unraveling the mystery of auxin-promoting femaleness in cucurbits","authors":"Liu Xiaofeng, Zhang Zhonghua, Sun jinjing","doi":"10.1093/hr/uhaf354","DOIUrl":"https://doi.org/10.1093/hr/uhaf354","url":null,"abstract":"The female flower gives rise to the fruit/seed and thus directly affects crop yield in unisexual plants. Both ethylene and auxin promote femaleness in cucurbits. However, how auxin regulates sex determination has been an open question over half a century. The recent publication (Han et al., Science, 2025) identified auxin response factor CsARF3 as a crucial player in auxin-promoting femaleness, and revealed a reciprocal relationship between auxin and ethylene during female flower determination.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"13 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145813204","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}
Extreme heat driven by climate change poses a catastrophic threat to global vegetable production, undermining nutritional security because of the heightened physiological sensitivity and succulent tissues of these crops.This review synthesizes the multi-stage impacts of heat stress across critical developmental phases-from germination to reproduction-emphasizing morphological impairments (such as leaf wilting and floral abortion), physiological disruptions (including photosynthetic inhibition and oxidative damage). We systematically dissect thermotolerance mechanisms in vegetables, highlighting transcriptional reprogramming by HSFs, WRKY, and NAC transcription factors; chaperone-mediated proteostasis via HSPs; epigenetic remodeling; Ca2+-ROS signaling pathways and the role of phase separation dynamics. Importantly, we propose six strategic pathways to develop heat-resilient vegetables: harnessing natural variation through pan-genome-driven allele mining; employing biotechnological interventions such as CRISPR-mediated editing and synthetic promoters; engineering multi-stress tolerance by targeting conserved “core response” pathways; exploiting epigenetic memory to achieve transgenerational resilience; optimizing source-sink dynamics with Climate-Responsive Carbon Optimization ; and applying plant growth regulators and nanotechnology to enhance thermotolerance. Together, these strategies chart a clear roadmap for climate-smart vegetable breeding, and call for interdisciplinary collaboration to translate molecular discoveries into practical breeding approaches for sustainable food systems under escalating thermal extremes.
{"title":"Molecular Mechanisms and Breeding Strategies for Heat Tolerance in Vegetable Crops under Global Warming","authors":"Yanlong Li, Xi Zhang, Chan Xia, Ting Wu, Yuyu Gao, Lingen Zeng, Zhuoxuan Wu, Xiongze Dai, Fang Yuan, Feng Liu, Sha Yang, Xuexiao Zou","doi":"10.1093/hr/uhaf309","DOIUrl":"https://doi.org/10.1093/hr/uhaf309","url":null,"abstract":"Extreme heat driven by climate change poses a catastrophic threat to global vegetable production, undermining nutritional security because of the heightened physiological sensitivity and succulent tissues of these crops.This review synthesizes the multi-stage impacts of heat stress across critical developmental phases-from germination to reproduction-emphasizing morphological impairments (such as leaf wilting and floral abortion), physiological disruptions (including photosynthetic inhibition and oxidative damage). We systematically dissect thermotolerance mechanisms in vegetables, highlighting transcriptional reprogramming by HSFs, WRKY, and NAC transcription factors; chaperone-mediated proteostasis via HSPs; epigenetic remodeling; Ca2+-ROS signaling pathways and the role of phase separation dynamics. Importantly, we propose six strategic pathways to develop heat-resilient vegetables: harnessing natural variation through pan-genome-driven allele mining; employing biotechnological interventions such as CRISPR-mediated editing and synthetic promoters; engineering multi-stress tolerance by targeting conserved “core response” pathways; exploiting epigenetic memory to achieve transgenerational resilience; optimizing source-sink dynamics with Climate-Responsive Carbon Optimization ; and applying plant growth regulators and nanotechnology to enhance thermotolerance. Together, these strategies chart a clear roadmap for climate-smart vegetable breeding, and call for interdisciplinary collaboration to translate molecular discoveries into practical breeding approaches for sustainable food systems under escalating thermal extremes.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"11 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145801224","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}
ASMT/COMT, as a key rate-limiting enzyme regulating melatonin biosynthesis, has garnered significant attention. This study investigates the evolutionary mechanisms of the ASMT/COMT gene family in melatonin biosynthesis. A total of 28 010 ASMT/COMT genes from 1052 species were identified through an integrated approach combining large-scale identifications and analyses. At the pan-genome level, we identified 5186, 336, 2137 and 1814 ASMT/COMT genes respectively in Triticum aestivum, Aegilops tauschii, diploid and tetraploid Solanum tuberosum haplotype genomes (247, 86, 670 and 96 orthologous gene groups). Expansion patterns of the ASMT/COMT gene family were explored through synteny networks in 104 Poaceae and 88 Solanaceae plants. Further investigation of copy number variation (CNV) in the 1052 species, along with a focused analysis of hexaploid wheat and its diploid progenitor Ae. tauschii, indicated a functional divergence linked to gene dosage. The catalytically efficient COMT is maintained at low-copy conditions, whereas the less active ASMT is amplified under high-copy conditions. Intriguingly, in polyploid potatoes, the total ASMT/COMT copy number was lower in tetraploids than in diploids, suggesting a distinct dosage balance mechanism operating in polyploids. In contrast, the melatonin receptor CAND2 consistently remained in a low-copy state, with no significant correlation to ASMT/COMT copy number. Expression analysis revealed that COMT is generally expressed at higher levels than ASMT, highlighting a compensatory relationship between gene dosage and transcriptional regulation. Collectively, our findings uncover a dosage-balance mechanism that fine-tunes melatonin biosynthetic homeostasis through coordinated copy number variation and expression regulation, offering a new perspective on the evolution of metabolic enzymes.
{"title":"Large-scale plant genomic identification and analysis uncover ASMT/COMT copy number variation driving melatonin dosage balance","authors":"Shuotong Liu, Pei Yu","doi":"10.1093/hr/uhaf348","DOIUrl":"https://doi.org/10.1093/hr/uhaf348","url":null,"abstract":"ASMT/COMT, as a key rate-limiting enzyme regulating melatonin biosynthesis, has garnered significant attention. This study investigates the evolutionary mechanisms of the ASMT/COMT gene family in melatonin biosynthesis. A total of 28 010 ASMT/COMT genes from 1052 species were identified through an integrated approach combining large-scale identifications and analyses. At the pan-genome level, we identified 5186, 336, 2137 and 1814 ASMT/COMT genes respectively in Triticum aestivum, Aegilops tauschii, diploid and tetraploid Solanum tuberosum haplotype genomes (247, 86, 670 and 96 orthologous gene groups). Expansion patterns of the ASMT/COMT gene family were explored through synteny networks in 104 Poaceae and 88 Solanaceae plants. Further investigation of copy number variation (CNV) in the 1052 species, along with a focused analysis of hexaploid wheat and its diploid progenitor Ae. tauschii, indicated a functional divergence linked to gene dosage. The catalytically efficient COMT is maintained at low-copy conditions, whereas the less active ASMT is amplified under high-copy conditions. Intriguingly, in polyploid potatoes, the total ASMT/COMT copy number was lower in tetraploids than in diploids, suggesting a distinct dosage balance mechanism operating in polyploids. In contrast, the melatonin receptor CAND2 consistently remained in a low-copy state, with no significant correlation to ASMT/COMT copy number. Expression analysis revealed that COMT is generally expressed at higher levels than ASMT, highlighting a compensatory relationship between gene dosage and transcriptional regulation. Collectively, our findings uncover a dosage-balance mechanism that fine-tunes melatonin biosynthetic homeostasis through coordinated copy number variation and expression regulation, offering a new perspective on the evolution of metabolic enzymes.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"155 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145770731","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}
Fruit ripening is a highly coordinated developmental process that transforms immature fruits into edible organs adapted for seed dispersal and human consumption. Although transcriptional regulation has long been acknowledged as fundamental mechanism underlying ripening control, accumulating evidence now indicates that post-translational modifications (PTMs) function as master regulatory switches that precisely control protein activity, stability, and interactions. PTMs such as phosphorylation, ubiquitination, acetylation, redox modifications, and methylation establish dynamic regulatory networks that integrate hormonal signals, metabolic fluxes, and environmental signals to control the complex biochemical and physiological changes during fruit ripening. This review summarizes current understanding of PTM-mediated regulation in both climacteric and non-climacteric fruits, emphasizing how modification cascades control key processes including ethylene signaling, cell wall remodeling, pigment accumulation, and stress responses. We explore emerging crosstalk networks in which multiple PTMs target important proteins to form complex molecular switches, and discuss recent methodological advances that facilitate systems-level analysis of PTM. Integrating PTM research with precision agriculture and biotechnology offers promising approaches for improving fruit quality, extending shelf life, and enhancing stress tolerance in the context of global climate change.
{"title":"Protein Post-translational Modifications: Key Switches Coordinating Fruit Ripening Regulatory Networks","authors":"Xiaojing Li, Qian Li, Guozheng Qin, Bingbing Li","doi":"10.1093/hr/uhaf351","DOIUrl":"https://doi.org/10.1093/hr/uhaf351","url":null,"abstract":"Fruit ripening is a highly coordinated developmental process that transforms immature fruits into edible organs adapted for seed dispersal and human consumption. Although transcriptional regulation has long been acknowledged as fundamental mechanism underlying ripening control, accumulating evidence now indicates that post-translational modifications (PTMs) function as master regulatory switches that precisely control protein activity, stability, and interactions. PTMs such as phosphorylation, ubiquitination, acetylation, redox modifications, and methylation establish dynamic regulatory networks that integrate hormonal signals, metabolic fluxes, and environmental signals to control the complex biochemical and physiological changes during fruit ripening. This review summarizes current understanding of PTM-mediated regulation in both climacteric and non-climacteric fruits, emphasizing how modification cascades control key processes including ethylene signaling, cell wall remodeling, pigment accumulation, and stress responses. We explore emerging crosstalk networks in which multiple PTMs target important proteins to form complex molecular switches, and discuss recent methodological advances that facilitate systems-level analysis of PTM. Integrating PTM research with precision agriculture and biotechnology offers promising approaches for improving fruit quality, extending shelf life, and enhancing stress tolerance in the context of global climate change.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"29 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145760113","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}
Horticultural and medicinal plants are important for their economic and pharmacological value; however, their quality traits are severely affected by abiotic stresses. The mitogen-activated protein kinase (MAPK) cascade is an evolutionarily conserved signaling module that links abiotic-stress signals to the regulation of plant quality traits. While the roles of MAPKs in growth, phytohormone signaling, and immunity are well established, a comprehensive review that integrates MAPK functions in abiotic-stress responses and secondary metabolism, particularly in horticultural and medicinal plants, is still lacking. In this review, we systematically summarize (1) the composition, classification, and phylogenetic relationships of MAPKs in horticultural and medicinal plants; (2) their mechanistic involvement in abiotic-stress responses, particularly to salt, drought, and extreme temperatures; (3) recent advances in understanding how MAPK-mediated signaling governs secondary metabolite accumulation; and (4) a unified framework that presents MAPKs as a key bridge between stress responses and metabolic reprogramming. These insights provide a foundation for MAPK-targeted breeding and engineering strategies that enhance stress tolerance and improve quality traits in horticultural and medicinal plants through precise pathway manipulation.
{"title":"MAPK regulates secondary metabolism and abiotic stress in horticultural and medicinal plants","authors":"Shuanglu Liu, Minghui Xing, Xiaojian Yin","doi":"10.1093/hr/uhaf350","DOIUrl":"https://doi.org/10.1093/hr/uhaf350","url":null,"abstract":"Horticultural and medicinal plants are important for their economic and pharmacological value; however, their quality traits are severely affected by abiotic stresses. The mitogen-activated protein kinase (MAPK) cascade is an evolutionarily conserved signaling module that links abiotic-stress signals to the regulation of plant quality traits. While the roles of MAPKs in growth, phytohormone signaling, and immunity are well established, a comprehensive review that integrates MAPK functions in abiotic-stress responses and secondary metabolism, particularly in horticultural and medicinal plants, is still lacking. In this review, we systematically summarize (1) the composition, classification, and phylogenetic relationships of MAPKs in horticultural and medicinal plants; (2) their mechanistic involvement in abiotic-stress responses, particularly to salt, drought, and extreme temperatures; (3) recent advances in understanding how MAPK-mediated signaling governs secondary metabolite accumulation; and (4) a unified framework that presents MAPKs as a key bridge between stress responses and metabolic reprogramming. These insights provide a foundation for MAPK-targeted breeding and engineering strategies that enhance stress tolerance and improve quality traits in horticultural and medicinal plants through precise pathway manipulation.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"20 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145765424","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}
Changjian Fa, Guijia Wang, Wenqi Pan, Yu Wang, Jincan Che, Ang Dong, Dengcheng Yang, Rongling Wu, Shing-Tung Yau, Lidan Sun
Complex traits are controlled by many unknown genes, making it difficult to elucidate a global picture of the genotype-phenotype map. Here, we develop a statistical mechanics model to contextualize all possible genes into informative, dynamic, omnidirectional and personalized idopNetworks. This model, derived from the combination of functional mapping and evolutionary game theory, can visualize and trace how genes act and interact with each other to shape the genetic architecture of complex traits. The model can estimate changes in the genotypic value of one gene due to the influence of other genes, specifically on individual subjects, surpassing traditional quantitative genetic studies that can only capture the marginal effect of a gene at the population level. We reconstruct growth idopNetworks from a genome-wide mapping data in a woody plant, mei, identifying unique genetic interaction architecture that distinguishes between fast-growing trees and slow-growing trees. We perform computer simulation to validate the statistical power of the model. IdopNetworks can disentangle the genetic control mechanisms of complex traits and provide guidance on how to alter phenotypic values of specific individuals by promoting or inhibiting the expression of interactive genes.
{"title":"An omnigenic interactome model to chart the genetic architecture of individual plants","authors":"Changjian Fa, Guijia Wang, Wenqi Pan, Yu Wang, Jincan Che, Ang Dong, Dengcheng Yang, Rongling Wu, Shing-Tung Yau, Lidan Sun","doi":"10.1093/hr/uhaf345","DOIUrl":"https://doi.org/10.1093/hr/uhaf345","url":null,"abstract":"Complex traits are controlled by many unknown genes, making it difficult to elucidate a global picture of the genotype-phenotype map. Here, we develop a statistical mechanics model to contextualize all possible genes into informative, dynamic, omnidirectional and personalized idopNetworks. This model, derived from the combination of functional mapping and evolutionary game theory, can visualize and trace how genes act and interact with each other to shape the genetic architecture of complex traits. The model can estimate changes in the genotypic value of one gene due to the influence of other genes, specifically on individual subjects, surpassing traditional quantitative genetic studies that can only capture the marginal effect of a gene at the population level. We reconstruct growth idopNetworks from a genome-wide mapping data in a woody plant, mei, identifying unique genetic interaction architecture that distinguishes between fast-growing trees and slow-growing trees. We perform computer simulation to validate the statistical power of the model. IdopNetworks can disentangle the genetic control mechanisms of complex traits and provide guidance on how to alter phenotypic values of specific individuals by promoting or inhibiting the expression of interactive genes.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"166 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145759445","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}
Cucumber is an important vegetable crop with thermophilic but heat-sensitive growth characteristics. Heat stress threatens cucumber growth and development, leading to a decline in both quality and yield. However, the evaluation system and molecular mechanism of long-term heat tolerance remain unclear. Here, an evaluation system in response to long-term heat stress was established, and chlorophyll a content and catalase (CAT) activity were identified as key evaluation indices for determining the heat tolerance of cucumber seedlings. Transcriptomic and physiological analyses revealed that sugar metabolism played a pivotal role in the heat response. Notably, the expression of CsIAGLU (Indoleacetic Acid glucosyltransferase) was significantly up-regulated in heat-tolerant genotype PS76, whereas it was not induced in the heat-sensitive genotype PWRG. Loss-of-function of CsIAGLU by gene editing resulted in increased sensitivity to heat stress along with higher sugar contents, accelerated stomatal closure and chlorophyll degradation. Furthermore, CsDREB2C.L, a positive regulator of heat stress response, directly bound to the CsIAGLU promoter to enhance its expression. Overexpression of CsDREB2C.L and CsIAGLU maintained stable sugar contents, thereby keeping stomatal opening and sustained leaf greening to resist heat stress. Taken together, our findings provide valuable insights into the mechanism of heat resistance in cucumber.
{"title":"The DREB2C.L-IAGLU module contributes to long-term heat stress via sugar metabolism in cucumber","authors":"Xiao Ma, Chuang Li, Yong Yuan, Xitong Zhong, Yafei Huang, Jiacai Chen, Yan Geng, Yuyan Li, Zhaoyang Zhou, Ming Xin, Xiaolan Zhang, Jianyu Zhao","doi":"10.1093/hr/uhaf341","DOIUrl":"https://doi.org/10.1093/hr/uhaf341","url":null,"abstract":"Cucumber is an important vegetable crop with thermophilic but heat-sensitive growth characteristics. Heat stress threatens cucumber growth and development, leading to a decline in both quality and yield. However, the evaluation system and molecular mechanism of long-term heat tolerance remain unclear. Here, an evaluation system in response to long-term heat stress was established, and chlorophyll a content and catalase (CAT) activity were identified as key evaluation indices for determining the heat tolerance of cucumber seedlings. Transcriptomic and physiological analyses revealed that sugar metabolism played a pivotal role in the heat response. Notably, the expression of CsIAGLU (Indoleacetic Acid glucosyltransferase) was significantly up-regulated in heat-tolerant genotype PS76, whereas it was not induced in the heat-sensitive genotype PWRG. Loss-of-function of CsIAGLU by gene editing resulted in increased sensitivity to heat stress along with higher sugar contents, accelerated stomatal closure and chlorophyll degradation. Furthermore, CsDREB2C.L, a positive regulator of heat stress response, directly bound to the CsIAGLU promoter to enhance its expression. Overexpression of CsDREB2C.L and CsIAGLU maintained stable sugar contents, thereby keeping stomatal opening and sustained leaf greening to resist heat stress. Taken together, our findings provide valuable insights into the mechanism of heat resistance in cucumber.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"30 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145717321","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}
Xufang Tian, Siyu Yang, Siyu Wang, Wei Li, Guofeng Li, Shi Zhang, Jin Wang, Di Liu, Yifei Liu
Coptis species are rich in protoberberine-type benzylisoquinoline alkaloids (BIAs). However, the differential BIA accumulation between C. chinensis and C. teeta, two primary botanical sources of traditional Chinese medicine “Huanglian”, remains mechanistically poorly understood. Here, we combined widely-targeted metabolomics, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), histological characterization, and transcriptomic analyses to investigate the mechanisms underlying the specialized BIA accumulation in C. chinensis versus C. teeta. Clearly, we observed significantly elevated BIA accumulation in C. chinensis rhizomes compared to C. teeta, in particular the preferential BIA localization within the cortical tissues of C. chinensis rhizomes, consistent to the anatomically expanded cortical and xylem regions. This structural specialization facilitates BIA compartmental distribution patterns. Integrated transcriptomic-metabolomic analysis further constructed a BIA biosynthetic regulatory network, identifying key transcription factors (TFs) that synergistically promote BIA accumulation in C. chinensis rhizomes, establishing their roles as speciation-associated regulators of medicinal quality divergence between C. chinensis and C. teeta. Overall, this study provides the first integrated anatomical and transcriptional framework explaining interspecies differences in BIA accumulation, enabling the development of quality improvement strategies for medicinal plants.
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