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.
{"title":"Multi-omics analysis reveals structural and transcriptional regulation specificity underlying differential benzylisoquinoline alkaloid accumulation in Coptis","authors":"Xufang Tian, Siyu Yang, Siyu Wang, Wei Li, Guofeng Li, Shi Zhang, Jin Wang, Di Liu, Yifei Liu","doi":"10.1093/hr/uhaf338","DOIUrl":"https://doi.org/10.1093/hr/uhaf338","url":null,"abstract":"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.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"11 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145753134","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}
Phalaenopsis orchids are one of the most important ornamental crops, prized for their beautiful flowers and long flowering phase. Hundreds of commercially available cultivars display a remarkable range of variation in key horticultural traits, including inflorescence type, floral size, and color patterning. While most current cultivars have been developed through cross-breeding or mutation breeding, genetic homogenization has become a growing concern. This is largely due to extensive hybridization among existing cultivars, which are predominantly derived from a limited number of parental species. Additionally, trait linkage in Phal. can hinder the integration of desirable characteristics in progeny. Therefore, there is an urgent need to decipher the genetic programs governing key horticultural traits to facilitate both conventional and molecular breeding. Despite significant research efforts, progress has been hampered by several resource limitations. These include a scarcity of high-quality genome assemblies, the lack of stable genetic transformation systems, and insufficient materials for molecular biology studies—a challenge exacerbated by the plant's relatively long life cycle. Consequently, the molecular mechanisms underlying the formation and diversity of most important horticultural traits in Phal. orchids remain largely unexplored. This review summarizes recent research advances, with a primary focus on the key floral traits in Phal. orchids, including inflorescence type, flowering time, floral organ organization, color patterning, size, longevity, scent, organ shape, cuticle production and wax biosynthesis. Furthermore, we offer perspectives on future research directions aimed at elucidating the genetic basis for the remarkable diversity of these traits and advancing molecular breeding in Phal. orchids.
{"title":"Molecular mechanisms underlying floral trait formation in Phalaenopsis orchids","authors":"Fei Wang, Xinyi Zuo, Angel Wingho SZE, Zhimei Li, Tao Xie, Hongyan Shan, Rui Zhang, Ruidong Jia, Hongzhi Kong, Peipei Wang","doi":"10.1093/hr/uhaf340","DOIUrl":"https://doi.org/10.1093/hr/uhaf340","url":null,"abstract":"Phalaenopsis orchids are one of the most important ornamental crops, prized for their beautiful flowers and long flowering phase. Hundreds of commercially available cultivars display a remarkable range of variation in key horticultural traits, including inflorescence type, floral size, and color patterning. While most current cultivars have been developed through cross-breeding or mutation breeding, genetic homogenization has become a growing concern. This is largely due to extensive hybridization among existing cultivars, which are predominantly derived from a limited number of parental species. Additionally, trait linkage in Phal. can hinder the integration of desirable characteristics in progeny. Therefore, there is an urgent need to decipher the genetic programs governing key horticultural traits to facilitate both conventional and molecular breeding. Despite significant research efforts, progress has been hampered by several resource limitations. These include a scarcity of high-quality genome assemblies, the lack of stable genetic transformation systems, and insufficient materials for molecular biology studies—a challenge exacerbated by the plant's relatively long life cycle. Consequently, the molecular mechanisms underlying the formation and diversity of most important horticultural traits in Phal. orchids remain largely unexplored. This review summarizes recent research advances, with a primary focus on the key floral traits in Phal. orchids, including inflorescence type, flowering time, floral organ organization, color patterning, size, longevity, scent, organ shape, cuticle production and wax biosynthesis. Furthermore, we offer perspectives on future research directions aimed at elucidating the genetic basis for the remarkable diversity of these traits and advancing molecular breeding in Phal. orchids.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"13 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145711450","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}
Nan Shan, Yao Xiao, Tianyao Li, Putao Wang, Asjad Ali, Jingyu Sun, Shenglin Wang, Qianglong Zhu, Tianxu Cao, Sha Luo, Jiali Lin, Zihao Li, Qinghong Zhou, Yingjin Huang
Chinese yam (Dioscorea polystachya) is extensively cultivated for nutritional and medicinal applications. However, the lack of a high-quality reference genome has hindered molecular genetic analysis and breeding advancements. Here, we present a haplotype-resolved chromosome-level assembly for this autotetraploid species, featuring a 1.56-Gb genome anchored to 80 chromosomes across four haplotypes and comprising 95,668 protein-coding genes. Following divergence from D. alata about 4.64 million years ago (Mya), D. polystachya underwent a specific whole-genome duplication ~1.42 Mya, resulting in an autotetraploid species without subgenomic dominance. Notably, the biosynthetic pathway genes of dioscin, an important steroidal saponin primarily accumulating in tubers, were generally over-retained in D. polystachya compared to the diploid species D. alata. Of these genes, 7-dehydrocholesterol reductase (Dp7-DR) promoted the accumulation of dioscin, exhibiting tuber-specific expression and strong inducibility by abscisic acid, based on transcriptome and gene function analyses. We determined that the transcription factor DpbZIP12 activates Dp7-DR transcription, as supported by yeast one-hybrid, dual-luciferase reporter, and electrophoretic mobility shift assays. Notably, overexpressing Dp7-DR or DpbZIP12 resulted in lower cholesterol levels and elevated dioscin levels, while silencing either gene produced opposite metabolic profiles. These findings delineate promising targets for manipulating dioscin content and expand genetic resources for enhancing yam nutritional quality.
{"title":"A haplotype-resolved chromosome-level genome assembly of autotetraploid Chinese yam ( Dioscorea polystachya ) elucidates dioscin biosynthesis and regulation","authors":"Nan Shan, Yao Xiao, Tianyao Li, Putao Wang, Asjad Ali, Jingyu Sun, Shenglin Wang, Qianglong Zhu, Tianxu Cao, Sha Luo, Jiali Lin, Zihao Li, Qinghong Zhou, Yingjin Huang","doi":"10.1093/hr/uhaf344","DOIUrl":"https://doi.org/10.1093/hr/uhaf344","url":null,"abstract":"Chinese yam (Dioscorea polystachya) is extensively cultivated for nutritional and medicinal applications. However, the lack of a high-quality reference genome has hindered molecular genetic analysis and breeding advancements. Here, we present a haplotype-resolved chromosome-level assembly for this autotetraploid species, featuring a 1.56-Gb genome anchored to 80 chromosomes across four haplotypes and comprising 95,668 protein-coding genes. Following divergence from D. alata about 4.64 million years ago (Mya), D. polystachya underwent a specific whole-genome duplication ~1.42 Mya, resulting in an autotetraploid species without subgenomic dominance. Notably, the biosynthetic pathway genes of dioscin, an important steroidal saponin primarily accumulating in tubers, were generally over-retained in D. polystachya compared to the diploid species D. alata. Of these genes, 7-dehydrocholesterol reductase (Dp7-DR) promoted the accumulation of dioscin, exhibiting tuber-specific expression and strong inducibility by abscisic acid, based on transcriptome and gene function analyses. We determined that the transcription factor DpbZIP12 activates Dp7-DR transcription, as supported by yeast one-hybrid, dual-luciferase reporter, and electrophoretic mobility shift assays. Notably, overexpressing Dp7-DR or DpbZIP12 resulted in lower cholesterol levels and elevated dioscin levels, while silencing either gene produced opposite metabolic profiles. These findings delineate promising targets for manipulating dioscin content and expand genetic resources for enhancing yam nutritional quality.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"112 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145717322","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}
Ou Chen, Rui Huang, Yao Xu, Shixiang Yao, Jian Ming, Kaifang Zeng
Green mold caused by Penicillium digitatum significantly impacts the citrus industry economically. Enhancing postharvest disease resistance in citrus fruit remains challenging due to the complex pathogen-citrus interaction. Previous researches have indicated that PgSCP, a small cysteine-rich secreted protein derived from Pichia galeiformis, activates resistance responses in citrus fruit. However, the precise molecular mechanisms underlying this effect remain unclear. This study showed that PgSCP enhances disease resistance gene expression and substance accumulation in citrus fruit. Additionally, potential citrus proteins that may interact with PgSCP was identified. Among these, four candidate transcription factors were identified: CsFAR1, CsMIKC, CsLBD, and CsGRAS. Subsequent validation demonstrated that PgSCP interacts with the citrus transcription factor CsFAR1. Transient overexpression analysis demonstrated that CsFAR1 positively regulates resistance to green mold, and CsFAR1 also enhances the disease resistance gene expression in citrus fruit. The CsFAR1 protein enhances resistance by activating DHAPS-1, GSH1, ACO1, INVA, PAL6, OMT, CYP73A16, CCOAOMT1, CYP73A4, PER16, and COMT1. These findings suggest that the yeast-secreted protein PgSCP may act as an elicitor that interacts with citrus transcription factors CsFAR1 to enhance host defense responses, thereby contributing to improved postharvest resistance to green mold.
{"title":"Yeast secreted protein PgSCP interacts with citrus transcription factors CsFAR1 to enhance green mold resistance in fruit","authors":"Ou Chen, Rui Huang, Yao Xu, Shixiang Yao, Jian Ming, Kaifang Zeng","doi":"10.1093/hr/uhaf339","DOIUrl":"https://doi.org/10.1093/hr/uhaf339","url":null,"abstract":"Green mold caused by Penicillium digitatum significantly impacts the citrus industry economically. Enhancing postharvest disease resistance in citrus fruit remains challenging due to the complex pathogen-citrus interaction. Previous researches have indicated that PgSCP, a small cysteine-rich secreted protein derived from Pichia galeiformis, activates resistance responses in citrus fruit. However, the precise molecular mechanisms underlying this effect remain unclear. This study showed that PgSCP enhances disease resistance gene expression and substance accumulation in citrus fruit. Additionally, potential citrus proteins that may interact with PgSCP was identified. Among these, four candidate transcription factors were identified: CsFAR1, CsMIKC, CsLBD, and CsGRAS. Subsequent validation demonstrated that PgSCP interacts with the citrus transcription factor CsFAR1. Transient overexpression analysis demonstrated that CsFAR1 positively regulates resistance to green mold, and CsFAR1 also enhances the disease resistance gene expression in citrus fruit. The CsFAR1 protein enhances resistance by activating DHAPS-1, GSH1, ACO1, INVA, PAL6, OMT, CYP73A16, CCOAOMT1, CYP73A4, PER16, and COMT1. These findings suggest that the yeast-secreted protein PgSCP may act as an elicitor that interacts with citrus transcription factors CsFAR1 to enhance host defense responses, thereby contributing to improved postharvest resistance to green mold.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"2 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145703831","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}
Regulating floral induction (FI) through the application of gibberellin (GA) biosynthesis inhibitors is a critical agricultural practice to prevent yield loss in fruit trees. We observed that mepiquat chloride (MC), a highly safe plant growth retardant, enhanced FI in mango. Nevertheless, the molecular mechanism by which MC facilitates FI remains elusive. Using two distinct treatments and varied stages during FI in mango (Mangifera indica L. ‘Tainong No.1’), 24 dynamic transcriptome profiles were constructed. Through pairwise comparisons and weighted gene co-expression network analysis (WGCNA), a regulatory network centered on the hub gene FLOWERING LOCUS T3 (MiFT3) was established. We further discovered MC-induced floral transition was associated with the decreases of GA20 and GA3 levels and the upregulation of MiGA2oxs (GA2 OXIDASES) expression, alongside the increase of abscisic acid (ABA) content and the upregulation of MiNCED1 (9-cis-epoxycarotenoid dioxygenase 1) and MiABI5-like7 (ABSCISIC ACID-INSENSITIVE 5-like7). Furthermore, biochemical assays and stable transgenic experiments were applied to confirmed that MiABI5-like7 activated the expression of MiFT3. Moreover, silencing MiABI5-like7 in mango buds delayed floral transition, while ectopic expression of MiABI5-like7 promoted early flowering. Additionally, exogenous ABA accelerated the floral transiton induced by MC, whereas an ABA inhibitor delayed floral transiton, which were associated with the expression levels of MiABI5-like7 and MiFT3. This study clarified the mechanism by which MC induced floral transition by inhibiting GA biosynthesis that activate MiABI5-like7-mediated signaling pathway, which provides novel insights into the regulatory network of FI in plants and offers a solution for solving the issue of insufficient flowering in warm winter climates.
{"title":"MiABI5-like7- MiFT3 regulatory module controls floral transition induced by mepiquat chloride in evergreen perennial mango ( Mangifera indica L.)","authors":"Wentian Xu, Bin Zheng, Hongxia Wu, Xiaolong He, Meng Gao, Kunliang Xie, Yanan Wang, Rulin Zhan, Yuyao Gao, Songbiao Wang, Xiaowei Ma","doi":"10.1093/hr/uhaf336","DOIUrl":"https://doi.org/10.1093/hr/uhaf336","url":null,"abstract":"Regulating floral induction (FI) through the application of gibberellin (GA) biosynthesis inhibitors is a critical agricultural practice to prevent yield loss in fruit trees. We observed that mepiquat chloride (MC), a highly safe plant growth retardant, enhanced FI in mango. Nevertheless, the molecular mechanism by which MC facilitates FI remains elusive. Using two distinct treatments and varied stages during FI in mango (Mangifera indica L. ‘Tainong No.1’), 24 dynamic transcriptome profiles were constructed. Through pairwise comparisons and weighted gene co-expression network analysis (WGCNA), a regulatory network centered on the hub gene FLOWERING LOCUS T3 (MiFT3) was established. We further discovered MC-induced floral transition was associated with the decreases of GA20 and GA3 levels and the upregulation of MiGA2oxs (GA2 OXIDASES) expression, alongside the increase of abscisic acid (ABA) content and the upregulation of MiNCED1 (9-cis-epoxycarotenoid dioxygenase 1) and MiABI5-like7 (ABSCISIC ACID-INSENSITIVE 5-like7). Furthermore, biochemical assays and stable transgenic experiments were applied to confirmed that MiABI5-like7 activated the expression of MiFT3. Moreover, silencing MiABI5-like7 in mango buds delayed floral transition, while ectopic expression of MiABI5-like7 promoted early flowering. Additionally, exogenous ABA accelerated the floral transiton induced by MC, whereas an ABA inhibitor delayed floral transiton, which were associated with the expression levels of MiABI5-like7 and MiFT3. This study clarified the mechanism by which MC induced floral transition by inhibiting GA biosynthesis that activate MiABI5-like7-mediated signaling pathway, which provides novel insights into the regulatory network of FI in plants and offers a solution for solving the issue of insufficient flowering in warm winter climates.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"8 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145703830","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}
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