Ning Li, Yunyun Cao, Peirong Li, Guize Wu, Yuxin Huang, Zhijun Zhang, Xiaoyun Xin, Weihong Wang, Xiuyun Zhao, Deshuang Zhang, Yangjun Yu, Fenglan Zhang, Ning Liu, Tongbing Su, Shuancang Yu
Downy mildew, caused by the biotrophic oomycete Hyaloperonospora parasitica, is one of the most devastating diseases affecting global Brassica production. Despite its significant impact, the molecular and cellular mechanisms underlying both compatible and incompatible interactions of H. parasitica and Brassica rapa remain poorly understood. In this study, we identified an H. parasitica RxLR effector, DM459, that demonstrates the ability to induce autophagy by targeting BraATG8i, a key component of autophagosome formation, as confirmed by multiple in vivo and in vitro assays. BraATG8i is a positive regulator of defense against downy mildew, which was determined by the BraATG8i overexpression and RNA interference in B. rapa. Furthermore, the effector DM459 interacts with BraATG8i as well as BraATG4, BraATG3, and BraATG7—core proteins required for autophagosome assembly. This interaction-enhanced autophagy contributed to elevated disease resistance. Moreover, both pathogen inoculation or DM459 presence stimulated salicylic acid (SA) biosynthesis, which in turn activated of BraATG8i expression and further elevated autophagy. Collectively, our results demonstrated that the effector DM459 triggers autophagy by directly targeting BraATG proteins and simultaneously activates SA signaling, which consequently enhances plant resistance to downy mildew.
{"title":"Targeting and activation of BraATG8i by an RxLR effector DM459 contribute to downy mildew resistance in Brassica rapa","authors":"Ning Li, Yunyun Cao, Peirong Li, Guize Wu, Yuxin Huang, Zhijun Zhang, Xiaoyun Xin, Weihong Wang, Xiuyun Zhao, Deshuang Zhang, Yangjun Yu, Fenglan Zhang, Ning Liu, Tongbing Su, Shuancang Yu","doi":"10.1093/hr/uhaf358","DOIUrl":"https://doi.org/10.1093/hr/uhaf358","url":null,"abstract":"Downy mildew, caused by the biotrophic oomycete Hyaloperonospora parasitica, is one of the most devastating diseases affecting global Brassica production. Despite its significant impact, the molecular and cellular mechanisms underlying both compatible and incompatible interactions of H. parasitica and Brassica rapa remain poorly understood. In this study, we identified an H. parasitica RxLR effector, DM459, that demonstrates the ability to induce autophagy by targeting BraATG8i, a key component of autophagosome formation, as confirmed by multiple in vivo and in vitro assays. BraATG8i is a positive regulator of defense against downy mildew, which was determined by the BraATG8i overexpression and RNA interference in B. rapa. Furthermore, the effector DM459 interacts with BraATG8i as well as BraATG4, BraATG3, and BraATG7—core proteins required for autophagosome assembly. This interaction-enhanced autophagy contributed to elevated disease resistance. Moreover, both pathogen inoculation or DM459 presence stimulated salicylic acid (SA) biosynthesis, which in turn activated of BraATG8i expression and further elevated autophagy. Collectively, our results demonstrated that the effector DM459 triggers autophagy by directly targeting BraATG proteins and simultaneously activates SA signaling, which consequently enhances plant resistance to downy mildew.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"11 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145894331","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}
Chuanzheng Wei, Shichao Sun, Yinzi Wang, Li Liu, Sofie Pearson, Yanbo Wang, Tashi Dorjee, Emma Mace, David Jordan, Yan Yang, Yongfu Tao
Cowpea (Vigna unguiculata) is a versatile legume crop providing a critical source of grain, vegetable and forage globally. Cultivated cowpea is classified into two main subspecies, subsp. sesquipedalis for fresh-pod vegetable and subsp. unguiculata for grain production. Here, we present two complete telomere-to-telomere (T2T) assemblies for the grain-type inbred lines HJD and vegetable-type FC6 through integrating PacBio HiFi reads, Oxford Nanopore ultra-long reads, and Hi-C data. The T2T genomes demonstrated improved contiguity, completeness, and accuracy compared to existing genomes, revealing clear telomeric and centromeric features. Comparative analysis of the T2T genomes highlighted inversions underlying subspecies divergence in cowpea. Evolutionary analysis uncovered contraction of gene families related to symbiosis in HJD, consist with its reduced root nodules compared to FC6. Distribution and composition of tandem repeat arrays and transposable elements in centromeric regions were largely conserved in cowpea, but displayed pronounced variation among Phaseoleae. Furthermore, frequent shifts of centromeric locations coincided with inversions found in Phaseoleae. Overall, this study provides a set of fundamental resources for cowpea improvement and enhances our understanding of cowpea subspecies divergence and genome evolution in Phaseoleae.
{"title":"Complete telomere-to-telomere genomes of cowpea reveal insights into centromere evolution in Phaseoleae","authors":"Chuanzheng Wei, Shichao Sun, Yinzi Wang, Li Liu, Sofie Pearson, Yanbo Wang, Tashi Dorjee, Emma Mace, David Jordan, Yan Yang, Yongfu Tao","doi":"10.1093/hr/uhaf359","DOIUrl":"https://doi.org/10.1093/hr/uhaf359","url":null,"abstract":"Cowpea (Vigna unguiculata) is a versatile legume crop providing a critical source of grain, vegetable and forage globally. Cultivated cowpea is classified into two main subspecies, subsp. sesquipedalis for fresh-pod vegetable and subsp. unguiculata for grain production. Here, we present two complete telomere-to-telomere (T2T) assemblies for the grain-type inbred lines HJD and vegetable-type FC6 through integrating PacBio HiFi reads, Oxford Nanopore ultra-long reads, and Hi-C data. The T2T genomes demonstrated improved contiguity, completeness, and accuracy compared to existing genomes, revealing clear telomeric and centromeric features. Comparative analysis of the T2T genomes highlighted inversions underlying subspecies divergence in cowpea. Evolutionary analysis uncovered contraction of gene families related to symbiosis in HJD, consist with its reduced root nodules compared to FC6. Distribution and composition of tandem repeat arrays and transposable elements in centromeric regions were largely conserved in cowpea, but displayed pronounced variation among Phaseoleae. Furthermore, frequent shifts of centromeric locations coincided with inversions found in Phaseoleae. Overall, this study provides a set of fundamental resources for cowpea improvement and enhances our understanding of cowpea subspecies divergence and genome evolution in Phaseoleae.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"14 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145847344","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}
Hideto Mochizuki, Mai F Minamikawa, Kosuke Hamazaki, Miyuki Kunihisa, Shigeki Moriya, Koji Noshita, Takeshi Hayashi, Yuichi Katayose, Toshiya Yamamoto, Hiroyoshi Iwata
Breeding perennial fruit trees like apple is constrained by long generation times and limited population sizes, which often lead to repeated use of a few elite cultivars and consequently narrow genetic diversity. To better understand how such selection process has shaped the current genetic structure, we applied gene-drop simulations—a pedigree-based method using known parentage and genetic maps—to a curated set of 185 apple cultivars used in Japanese breeding programs, genotyped with 11,786 genome-wide single nucleotide polymorphism (SNP) markers. This approach enabled us to quantify the expected distribution of founder haplotypes and identify genomic regions where observed founder allele frequencies significantly deviated from expectation, suggesting potential selection. Notably, biased regions overlapped with loci associated with key fruit traits such as fructose content, exemplified by an increase in haplotypes from ‘Golden Delicious.’ Furthermore, Gene Ontology analysis revealed enrichment for regions containing genes involved in stress-related and developmental functions, pointing to broader physiological traits under selection. Unlike traditional methods requiring phenotype data, our approach does not depend on trait measurements and can thus uncover cryptic selection signals, including traits that were not explicitly targeted during breeding. This method offers a framework for identifying overlooked genetic regions and underutilized founder alleles, which can be reintroduced to broaden the genetic base and improve breeding outcomes. Furthermore, the approach is adaptable to other perennial crops with available pedigree and genomic data. Our findings demonstrate the power of integrating pedigree structure with genomic information to reveal both historical and ongoing selection in structured breeding populations.
{"title":"Haplotype Bias Detection Using Pedigree-Based Transmission Simulation: Traces of Selection That Occurred in Apple Breeding","authors":"Hideto Mochizuki, Mai F Minamikawa, Kosuke Hamazaki, Miyuki Kunihisa, Shigeki Moriya, Koji Noshita, Takeshi Hayashi, Yuichi Katayose, Toshiya Yamamoto, Hiroyoshi Iwata","doi":"10.1093/hr/uhaf349","DOIUrl":"https://doi.org/10.1093/hr/uhaf349","url":null,"abstract":"Breeding perennial fruit trees like apple is constrained by long generation times and limited population sizes, which often lead to repeated use of a few elite cultivars and consequently narrow genetic diversity. To better understand how such selection process has shaped the current genetic structure, we applied gene-drop simulations—a pedigree-based method using known parentage and genetic maps—to a curated set of 185 apple cultivars used in Japanese breeding programs, genotyped with 11,786 genome-wide single nucleotide polymorphism (SNP) markers. This approach enabled us to quantify the expected distribution of founder haplotypes and identify genomic regions where observed founder allele frequencies significantly deviated from expectation, suggesting potential selection. Notably, biased regions overlapped with loci associated with key fruit traits such as fructose content, exemplified by an increase in haplotypes from ‘Golden Delicious.’ Furthermore, Gene Ontology analysis revealed enrichment for regions containing genes involved in stress-related and developmental functions, pointing to broader physiological traits under selection. Unlike traditional methods requiring phenotype data, our approach does not depend on trait measurements and can thus uncover cryptic selection signals, including traits that were not explicitly targeted during breeding. This method offers a framework for identifying overlooked genetic regions and underutilized founder alleles, which can be reintroduced to broaden the genetic base and improve breeding outcomes. Furthermore, the approach is adaptable to other perennial crops with available pedigree and genomic data. Our findings demonstrate the power of integrating pedigree structure with genomic information to reveal both historical and ongoing selection in structured breeding populations.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"184 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145830045","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}
Camellia sinensis Fuding Dahaocha, a triploid white tea cultivar widely cultivated in south China, exhibits distinctive traits including dense leaf trichomes, early sprouting, and robust stress resistance. Here, we present the first high-quality chromosome-level genome assembly of this triploid variety, resolved through integrated PacBio long-read sequencing and Hi-C scaffolding. The genome assembly spans 45 chromosomes with a scaffold N50 of 182 Mbp. A total of 149 455 gene models were annotated and mapped to chromosomes, among which 30 568 were identified as protein-coding genes. The genome features high repetitiveness (65.9% TEs), heterozygosity, and three distinct haplotype sets with substantial allelic variation (17 601 tri-allelic genes), with the retained haplotype-specific genes potentially contributing to regulatory complexity through dosage effects. Genome completeness assessment revealed a BUSCO completeness of 99.0% (2303 out of 2326 conserved core genes identified), which included 40 single-copy (1.7%) and 2263 duplicated (97.3%) genes. Evolutionary analyses indicated conserved relationships among the three homologous chromosome sets. We also performed single-nucleus RNA sequencing on a sufficiently large pooled sample of leaf tissues to study trichome development, overcoming technical limitations posed by secondary metabolites and low protoplast isolation efficiency. This yielded a single-cell atlas for woody plants, identifying 35 trichome-specific marker genes and modeling developmental trajectories during epidermal differentiation. Functional validation identified CsCUT1 as a suppressor of trichome branching and CsMYB4 as a negative regulator of trichome initiation. Cell cycle analysis showed G2-phase dominance in developing trichomes. These findings provide a genetic framework for trichome development and offer resources for tea breeding.
{"title":"Exploring the developmental mechanisms of tea plant Trichomes using genomics and single-cell transcriptome sequencing","authors":"Xuming Deng, Yajun Tang, Qing Zhang, Weilong Kong, Xiying Lin, Xianyu Chen, Zhidan Chen, Xintang Zhang, Weijiang Sun","doi":"10.1093/hr/uhaf352","DOIUrl":"https://doi.org/10.1093/hr/uhaf352","url":null,"abstract":"Camellia sinensis Fuding Dahaocha, a triploid white tea cultivar widely cultivated in south China, exhibits distinctive traits including dense leaf trichomes, early sprouting, and robust stress resistance. Here, we present the first high-quality chromosome-level genome assembly of this triploid variety, resolved through integrated PacBio long-read sequencing and Hi-C scaffolding. The genome assembly spans 45 chromosomes with a scaffold N50 of 182 Mbp. A total of 149 455 gene models were annotated and mapped to chromosomes, among which 30 568 were identified as protein-coding genes. The genome features high repetitiveness (65.9% TEs), heterozygosity, and three distinct haplotype sets with substantial allelic variation (17 601 tri-allelic genes), with the retained haplotype-specific genes potentially contributing to regulatory complexity through dosage effects. Genome completeness assessment revealed a BUSCO completeness of 99.0% (2303 out of 2326 conserved core genes identified), which included 40 single-copy (1.7%) and 2263 duplicated (97.3%) genes. Evolutionary analyses indicated conserved relationships among the three homologous chromosome sets. We also performed single-nucleus RNA sequencing on a sufficiently large pooled sample of leaf tissues to study trichome development, overcoming technical limitations posed by secondary metabolites and low protoplast isolation efficiency. This yielded a single-cell atlas for woody plants, identifying 35 trichome-specific marker genes and modeling developmental trajectories during epidermal differentiation. Functional validation identified CsCUT1 as a suppressor of trichome branching and CsMYB4 as a negative regulator of trichome initiation. Cell cycle analysis showed G2-phase dominance in developing trichomes. These findings provide a genetic framework for trichome development and offer resources for tea breeding.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"36 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145829971","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}
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}
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