Abdulqader Jighly, Norman Munyengwa, Reem Joukhadar, Vanika Garg, Natalie Dillon, Rhys G R Copeland, Jugpreet Singh, Sukhwinder Singh, Christopher I Cazzonelli, Penghao Wang, Peter Prentis, Craig Hardner, Rajeev K Varshney
Genomic prediction (GP) in mango breeding faces challenges due to the species’ complex biology, long cycles, and limited reference populations. To accelerate genetic improvement, this study integrated data from diverse global populations to increase the reference population size. It included three mango collections reserved in Australia (225), USA (161), and China (224), totalling 610 individuals. Fruit weight (FW) and total soluble solids (TSS) were measured in multiple datasets, while several other traits were measured in specific datasets. We evaluated genetic diversity, performed genome-wide association studies (GWAS), and assessed GP accuracy using standard, genotype-by-environment (GxE), and multi-trait models, both within and across collections. Findings revealed a highly admixed genetic structure, with faster linkage disequilibrium (LD) decay in the Chinese collection, indicating higher genetic diversity. Data integration significantly enhanced GWAS power, identifying 19 quantitative trait loci (QTL) for FW and 9 for TSS. GxE models consistently achieved higher or comparable prediction accuracies for FW and TSS compared to the non-GxE models, especially when combining Australian and USA collections. This was not the case when predicting into or from the Chinese collection, mostly due to differences in the phenotyping protocol. While single-trait models performed comparably to multi-trait models in predicting new individuals (Coss-Validation: CV1), multi-trait models significantly improved prediction accuracy in scenarios with incomplete phenotypic records (CV2). This study demonstrates that strategic global data integration significantly enhances GWAS power and GP accuracy in mango. This collaborative approach is crucial for developing more efficient and accelerated breeding programs for mango and other perennial trees.
{"title":"Strategic global data integration to improve genomic prediction accuracy in trees breeding programs facing resource limitations, a case study in mango","authors":"Abdulqader Jighly, Norman Munyengwa, Reem Joukhadar, Vanika Garg, Natalie Dillon, Rhys G R Copeland, Jugpreet Singh, Sukhwinder Singh, Christopher I Cazzonelli, Penghao Wang, Peter Prentis, Craig Hardner, Rajeev K Varshney","doi":"10.1093/hr/uhag004","DOIUrl":"https://doi.org/10.1093/hr/uhag004","url":null,"abstract":"Genomic prediction (GP) in mango breeding faces challenges due to the species’ complex biology, long cycles, and limited reference populations. To accelerate genetic improvement, this study integrated data from diverse global populations to increase the reference population size. It included three mango collections reserved in Australia (225), USA (161), and China (224), totalling 610 individuals. Fruit weight (FW) and total soluble solids (TSS) were measured in multiple datasets, while several other traits were measured in specific datasets. We evaluated genetic diversity, performed genome-wide association studies (GWAS), and assessed GP accuracy using standard, genotype-by-environment (GxE), and multi-trait models, both within and across collections. Findings revealed a highly admixed genetic structure, with faster linkage disequilibrium (LD) decay in the Chinese collection, indicating higher genetic diversity. Data integration significantly enhanced GWAS power, identifying 19 quantitative trait loci (QTL) for FW and 9 for TSS. GxE models consistently achieved higher or comparable prediction accuracies for FW and TSS compared to the non-GxE models, especially when combining Australian and USA collections. This was not the case when predicting into or from the Chinese collection, mostly due to differences in the phenotyping protocol. While single-trait models performed comparably to multi-trait models in predicting new individuals (Coss-Validation: CV1), multi-trait models significantly improved prediction accuracy in scenarios with incomplete phenotypic records (CV2). This study demonstrates that strategic global data integration significantly enhances GWAS power and GP accuracy in mango. This collaborative approach is crucial for developing more efficient and accelerated breeding programs for mango and other perennial trees.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"391 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145903626","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}
Alicja Macko-Podgórni, Kinga Zygmuntowicz, Wojciech Wesołowski, Kornelia Kwolek, Marcelina Skrabucha, Emilia Data, Zuzanna Boczar, Zara Maria Lacera, Charles Nathan Hancock, Dariusz Grzebelus
Transposable elements constitute a large portion of plant genomes and, due to their ability to change their genomic localization, they largely contribute to genome evolution and adaptability. Miniature inverted-repeat transposable elements (MITEs), due to their small size and localization near genes, seem to be a major source of potential functional variability. Effects imposed byMITEson the expression of associated genesthrough redistributing cis-regulatory elements have been postulated, but our knowledge in this area still remains limited. We showed that MITEs in the carrot genome are enriched with binding sites for LHY/RVE transcription factors. Experimental validation using DcLHY-DAP-seq not only confirmed the enrichment of DcLHY binding sites within MITEs but also demonstrated that elements from the DcTourist_15 family likely play a key role in redistributing these transcription factor binding sites. We showed that insertional polymorphisms of DcTourist_15 correspond with changes in the expression of associated genes, both in control conditions and in response to heat stress. In addition to placing individual genes under the control of DcLHY/RVE transcription factors, DcTourist_15 copies were found in promoters of genes involved in sulfur metabolism and cysteine biosynthesis. The enrichment of rice MITEs in OsLHY binding sites suggests the phenomenon of MITE-driven rewiring of LHY/RVE regulation may be more widespread across the plant kingdom. Carrot MITEs, particularly those from the DcTourist_15 family, drive evolution of the carrot genome, especially in the context of stress responsiveness, as they possibly fine-tune gene expression by redistributing binding sites for transcription factors from the LHY/RVE family.
{"title":"Cis-regulatory effects of carrot miniature inverted-repeat transposable elements on the expression of genes controlled by LHY/RVE transcription factors","authors":"Alicja Macko-Podgórni, Kinga Zygmuntowicz, Wojciech Wesołowski, Kornelia Kwolek, Marcelina Skrabucha, Emilia Data, Zuzanna Boczar, Zara Maria Lacera, Charles Nathan Hancock, Dariusz Grzebelus","doi":"10.1093/hr/uhaf360","DOIUrl":"https://doi.org/10.1093/hr/uhaf360","url":null,"abstract":"Transposable elements constitute a large portion of plant genomes and, due to their ability to change their genomic localization, they largely contribute to genome evolution and adaptability. Miniature inverted-repeat transposable elements (MITEs), due to their small size and localization near genes, seem to be a major source of potential functional variability. Effects imposed byMITEson the expression of associated genesthrough redistributing cis-regulatory elements have been postulated, but our knowledge in this area still remains limited. We showed that MITEs in the carrot genome are enriched with binding sites for LHY/RVE transcription factors. Experimental validation using DcLHY-DAP-seq not only confirmed the enrichment of DcLHY binding sites within MITEs but also demonstrated that elements from the DcTourist_15 family likely play a key role in redistributing these transcription factor binding sites. We showed that insertional polymorphisms of DcTourist_15 correspond with changes in the expression of associated genes, both in control conditions and in response to heat stress. In addition to placing individual genes under the control of DcLHY/RVE transcription factors, DcTourist_15 copies were found in promoters of genes involved in sulfur metabolism and cysteine biosynthesis. The enrichment of rice MITEs in OsLHY binding sites suggests the phenomenon of MITE-driven rewiring of LHY/RVE regulation may be more widespread across the plant kingdom. Carrot MITEs, particularly those from the DcTourist_15 family, drive evolution of the carrot genome, especially in the context of stress responsiveness, as they possibly fine-tune gene expression by redistributing binding sites for transcription factors from the LHY/RVE family.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"121 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145894329","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}
Edda Francomano, Meriem Miyassa Aci, Saveria Mosca, Nesma Zakaria Mohamed, Giovanni Enrico Agosteo, Maria Giulia Li Destri Nicosia, Antonino Malacrinò, Leonardo Schena
Agriculture faces unprecedented challenges due to climate change, increasing food demand, and resource scarcity, which needs sustainable and innovative solutions. This review explores the emerging paradigm of holobiont biology (host and its microbiome as biological unit) in the context of emerging plant health challenges driven by global changes. We highlight three critical challenges: the rise of complex plant syndromes, the emergence and re-emergence of plant diseases, and the consequences of dysbiotic plant microbiomes. We discuss how microbiome-based strategies can enhance plant resilience, reduce reliance on agrochemicals, and foster sustainable agriculture. Integrating these strategies with advanced frameworks, such as holo-omics and machine learning, opens avenues for microbiome-based solutions to address agricultural challenges in the era of global changes, ensuring resilient crop systems and planetary health.
{"title":"Plant health in the era of global changes, holobiont biology, and microbiome-based solutions","authors":"Edda Francomano, Meriem Miyassa Aci, Saveria Mosca, Nesma Zakaria Mohamed, Giovanni Enrico Agosteo, Maria Giulia Li Destri Nicosia, Antonino Malacrinò, Leonardo Schena","doi":"10.1093/hr/uhaf364","DOIUrl":"https://doi.org/10.1093/hr/uhaf364","url":null,"abstract":"Agriculture faces unprecedented challenges due to climate change, increasing food demand, and resource scarcity, which needs sustainable and innovative solutions. This review explores the emerging paradigm of holobiont biology (host and its microbiome as biological unit) in the context of emerging plant health challenges driven by global changes. We highlight three critical challenges: the rise of complex plant syndromes, the emergence and re-emergence of plant diseases, and the consequences of dysbiotic plant microbiomes. We discuss how microbiome-based strategies can enhance plant resilience, reduce reliance on agrochemicals, and foster sustainable agriculture. Integrating these strategies with advanced frameworks, such as holo-omics and machine learning, opens avenues for microbiome-based solutions to address agricultural challenges in the era of global changes, ensuring resilient crop systems and planetary health.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"53 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145894330","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}
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}
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