Can Zeng, Jianjie He, Jianshuo Li, Shipeng Fan, Mingli Wu, Xin Cheng, Yutian Xia, Dongqing Zhang, Xiaoling Dun, Maoteng Li
Rapeseed (Brassica napus L.) is one of the most important oil crops worldwide. In our previous work, we generated a high-throughput CRISPR library whereby a knockout collection was established for rapeseed breeding and functional genomics. However, the collection remains small and several promising candidate genes still await functional validation. Here, we report an update of this collection by constructing a small-scale CRISPR mutant library based on the elite commercial cultivar Zhongshuang 11 (ZS11). We first generated 326 independent T0 lines using an optimized protocol for ZS11 transformation and regeneration with a high positive rate of 94.2%. Analysis of the editing outcomes revealed a mutagenesis frequency of 68.4%. We then phenotyped this new collection and unraveled possible key genes underlying the variations in seed oil content (SOC) and plant height. Finally, we functionally validated BnFAB1B and BnEDA32, two candidate genes identified from our knockout collection. The results confirmed that loss-of-function of BnFAB1B significantly increases SOC, indicating its great agronomic potential, whereas knockout of the nuclear-localized BnEDA32 severely disrupts seed oil accumulation. This study provides a valuable knockout collection of the elite cultivar ZS11 and new genes for creating superior rapeseed germplasm.
{"title":"A Small-scale CRISPR Mutant Library in Rapeseed of Commercial Cultivar Zhongshuang 11","authors":"Can Zeng, Jianjie He, Jianshuo Li, Shipeng Fan, Mingli Wu, Xin Cheng, Yutian Xia, Dongqing Zhang, Xiaoling Dun, Maoteng Li","doi":"10.1093/hr/uhag087","DOIUrl":"https://doi.org/10.1093/hr/uhag087","url":null,"abstract":"Rapeseed (Brassica napus L.) is one of the most important oil crops worldwide. In our previous work, we generated a high-throughput CRISPR library whereby a knockout collection was established for rapeseed breeding and functional genomics. However, the collection remains small and several promising candidate genes still await functional validation. Here, we report an update of this collection by constructing a small-scale CRISPR mutant library based on the elite commercial cultivar Zhongshuang 11 (ZS11). We first generated 326 independent T0 lines using an optimized protocol for ZS11 transformation and regeneration with a high positive rate of 94.2%. Analysis of the editing outcomes revealed a mutagenesis frequency of 68.4%. We then phenotyped this new collection and unraveled possible key genes underlying the variations in seed oil content (SOC) and plant height. Finally, we functionally validated BnFAB1B and BnEDA32, two candidate genes identified from our knockout collection. The results confirmed that loss-of-function of BnFAB1B significantly increases SOC, indicating its great agronomic potential, whereas knockout of the nuclear-localized BnEDA32 severely disrupts seed oil accumulation. This study provides a valuable knockout collection of the elite cultivar ZS11 and new genes for creating superior rapeseed germplasm.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"12 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147360387","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}
Heng Wang, Lin Chai, Hongjun Yu, Hongxue Li, Debao Yi, Sufian Ikram, Tao Lu, Yang Li, Xueyong Yang, Weijie Jiang, Qiang Li
Drought tolerance is a pivotal trait for tomato (Solanum lycopersicum) genetic improvement, and enhancing the root:shoot ratio (R/S) serves as a core adaptive strategy for plants to cope with water deficit. While trehalose-6-phosphate phosphatase (TPP) genes are implicated in plant drought responses, their role in modulating R/S remains unclear. Here, we characterized SlTPP1 as a key positive regulator of drought tolerance in tomato. We found that drought stress dynamically induces SlTPP1 expression in roots while suppressing it in leaves. Mechanistically, SlTPP1 overexpression increases root soluble sugar content and upregulates night-specific expression of cell wall biosynthesis genes in roots to promote root growth, while concurrently suppressing the ethylene signaling pathway in leaves to increase R/S. Furthermore, we identified the transcription factor SlERF4 as a direct upstream repressor of SlTPP1. SlERF4 binds to the CE1 element (CACCG) in the SlTPP1 promoter and inhibits its transcription. CRISPR/Cas9-mediated knockout of SlERF4 results in enhanced drought tolerance, elevated SlTPP1 expression, increased R/S, and upregulation of root cell wall biosynthesis genes. Additionally, drought enhances ethylene biosynthesis in tomato leaves while concurrently reducing that in roots. Collectively, our study unveils a novel SlERF4-SlTPP1 regulatory module that enhances drought tolerance in tomato through the regulation of R/S, providing strategic targets for breeding drought-tolerant crops.
{"title":"A SlERF4-SlTPP1 module enhances drought tolerance in tomato by increasing root:shoot ratio","authors":"Heng Wang, Lin Chai, Hongjun Yu, Hongxue Li, Debao Yi, Sufian Ikram, Tao Lu, Yang Li, Xueyong Yang, Weijie Jiang, Qiang Li","doi":"10.1093/hr/uhag070","DOIUrl":"https://doi.org/10.1093/hr/uhag070","url":null,"abstract":"Drought tolerance is a pivotal trait for tomato (Solanum lycopersicum) genetic improvement, and enhancing the root:shoot ratio (R/S) serves as a core adaptive strategy for plants to cope with water deficit. While trehalose-6-phosphate phosphatase (TPP) genes are implicated in plant drought responses, their role in modulating R/S remains unclear. Here, we characterized SlTPP1 as a key positive regulator of drought tolerance in tomato. We found that drought stress dynamically induces SlTPP1 expression in roots while suppressing it in leaves. Mechanistically, SlTPP1 overexpression increases root soluble sugar content and upregulates night-specific expression of cell wall biosynthesis genes in roots to promote root growth, while concurrently suppressing the ethylene signaling pathway in leaves to increase R/S. Furthermore, we identified the transcription factor SlERF4 as a direct upstream repressor of SlTPP1. SlERF4 binds to the CE1 element (CACCG) in the SlTPP1 promoter and inhibits its transcription. CRISPR/Cas9-mediated knockout of SlERF4 results in enhanced drought tolerance, elevated SlTPP1 expression, increased R/S, and upregulation of root cell wall biosynthesis genes. Additionally, drought enhances ethylene biosynthesis in tomato leaves while concurrently reducing that in roots. Collectively, our study unveils a novel SlERF4-SlTPP1 regulatory module that enhances drought tolerance in tomato through the regulation of R/S, providing strategic targets for breeding drought-tolerant crops.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"228 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147329711","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}
Sunflower (Helianthus annuus L.) is one of the pioneer crops with extremely strong adaptability to adverse stresses, and its stress (such as high salinity) tolerance improvement will contribute to the utilization of abundant marginal land and promote sustainable development. However, the genetic determinants underlying response to salt stress are not fully understood. Here, we perform a genome-wide association study (GWAS) using 31 traits from a high-throughput platform in 342 oilseed sunflower accessions at the germination stage under salt stress conditions. We identify 359 significantly associated SNPs and 63 InDels corresponding to 424 and 83 candidate genes, respectively. One candidate gene, C-Repeat Binding Factor 4 (CBF4)-a member of the AP2/EREBP family transcription factor- directly binds to dehydration-responsive element (DRE) in the promoter region of its downstream target gene, High-Affinity K+ transporter 11 (HAK11), thereby activating its expression. This regulatory mechanism contributes to enhanced salt tolerance in sunflower by modulating established salt-responsive genetic pathways. Collectively, our findings provide new insights into salt tolerance mechanisms and offer valuable genetic resources for breeding salt-tolerant sunflower cultivars.
{"title":"Integrating high-throughput phenomics and GWAS unravels the HaCBF4- HaHAK11 module to regulate salt stress tolerance in sunflower ( Helianthus annuus L.)","authors":"Weijun Guo, Jiawei Qiu, Youling Zeng, Xinxin Li, Shurui Dong, Qinyang Li, Yushan Liu, Maohong Cai, Zhonghua Lei, Tao Chen","doi":"10.1093/hr/uhag081","DOIUrl":"https://doi.org/10.1093/hr/uhag081","url":null,"abstract":"Sunflower (Helianthus annuus L.) is one of the pioneer crops with extremely strong adaptability to adverse stresses, and its stress (such as high salinity) tolerance improvement will contribute to the utilization of abundant marginal land and promote sustainable development. However, the genetic determinants underlying response to salt stress are not fully understood. Here, we perform a genome-wide association study (GWAS) using 31 traits from a high-throughput platform in 342 oilseed sunflower accessions at the germination stage under salt stress conditions. We identify 359 significantly associated SNPs and 63 InDels corresponding to 424 and 83 candidate genes, respectively. One candidate gene, C-Repeat Binding Factor 4 (CBF4)-a member of the AP2/EREBP family transcription factor- directly binds to dehydration-responsive element (DRE) in the promoter region of its downstream target gene, High-Affinity K+ transporter 11 (HAK11), thereby activating its expression. This regulatory mechanism contributes to enhanced salt tolerance in sunflower by modulating established salt-responsive genetic pathways. Collectively, our findings provide new insights into salt tolerance mechanisms and offer valuable genetic resources for breeding salt-tolerant sunflower cultivars.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"24 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147360425","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 evolutionary history of the ANA-grade angiosperms provides a crucial window into the transition of early flowering plants. Within this group, the Nymphaeales (water lilies) are pivotal, yet a lack of gapless genomic resources has hindered research into their complex developmental and adaptive programs. In this study, we present a telomere-to-telomere (T2T), gap-free genome assembly of Nymphaea minuta, a miniature water lily endemic to Madagascar. Utilizing PacBio Revio HiFi and Hi-C technologies, we generated a 382 Mb assembly anchored to 14 chromosomes. Comparative analysis reveals a compact genome with lower levels of ancient polyploidization than other Nymphaeaceae. By integrating a comprehensive transcriptome atlas of 15 organs and developmental stages, we identified seven primary developmental trajectories and 1,179 organ-specific genes. Our analysis uncovered two critical regulatory models: Sequential Dual-Module Relay: In leaves, water fluctuation triggers an initial MAPK-signaling stress response, followed by a post-transcriptional "transcriptome reset" mediated by the RNA degradation pathway (LSM1/2 and ENOC) during severe drought. Energy-Program Coordination: Seed development is governed by a three-phase transition where the glyoxylate cycle (MLS) drives energy mobilization, while an ERF1-centered hub integrates ethylene, ABA, and JA signaling to balance rapid germination with immune defense. These findings provide a definitive genomic reference for basal angiosperms and elucidate the molecular networks enabling the survival and rapid development of these ancient aquatic herbs.
{"title":"A telomere-to-telomere genome assembly of Nymphaea minuta provides details into the developmental transcriptome atlas and adaptive regulatory mechanisms","authors":"Hongliang Chen, Yufan Liang, Jia-Yu Xue, Fei Chen","doi":"10.1093/hr/uhag085","DOIUrl":"https://doi.org/10.1093/hr/uhag085","url":null,"abstract":"The evolutionary history of the ANA-grade angiosperms provides a crucial window into the transition of early flowering plants. Within this group, the Nymphaeales (water lilies) are pivotal, yet a lack of gapless genomic resources has hindered research into their complex developmental and adaptive programs. In this study, we present a telomere-to-telomere (T2T), gap-free genome assembly of Nymphaea minuta, a miniature water lily endemic to Madagascar. Utilizing PacBio Revio HiFi and Hi-C technologies, we generated a 382 Mb assembly anchored to 14 chromosomes. Comparative analysis reveals a compact genome with lower levels of ancient polyploidization than other Nymphaeaceae. By integrating a comprehensive transcriptome atlas of 15 organs and developmental stages, we identified seven primary developmental trajectories and 1,179 organ-specific genes. Our analysis uncovered two critical regulatory models: Sequential Dual-Module Relay: In leaves, water fluctuation triggers an initial MAPK-signaling stress response, followed by a post-transcriptional \"transcriptome reset\" mediated by the RNA degradation pathway (LSM1/2 and ENOC) during severe drought. Energy-Program Coordination: Seed development is governed by a three-phase transition where the glyoxylate cycle (MLS) drives energy mobilization, while an ERF1-centered hub integrates ethylene, ABA, and JA signaling to balance rapid germination with immune defense. These findings provide a definitive genomic reference for basal angiosperms and elucidate the molecular networks enabling the survival and rapid development of these ancient aquatic herbs.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"107 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147360426","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}
Yanfeng Jia, Jiarui Li, Mengyao Wei, Chaofan Li, Jiawang Qin, Mengjie An, Quanlin Li
Apple (Malus domestica) is one of the most widely cultivated and consumed fruits worldwide, valued for its rich nutrition and health benefits. Cold limits apple tree growth, development, yield, and fruit quality. Understanding the regulatory networks of apple plants in response to cold stress is crucial for improving their cold tolerance. In this review, we summarize the molecular regulation of apple plants to withstand cold stress involving transcription cascade, hormone signal, reactive oxygen species (ROS) homeostasis, epigenetic control, and post-translational modifications, as well as the crosstalk pathway with drought, immune, and light. We also underscore the management strategies aimed at enhancing apple plants cold tolerance, including the utilization of wild germplasm resources, integration of multi-omics regulatory network, gene editing, molecular marker-assisted breeding, and rootstock grafting. This review provides a molecular basis for gene expression regulation strategies to improve apple trees cold tolerance.
{"title":"Regulatory insights underlying apple trees to cold stress","authors":"Yanfeng Jia, Jiarui Li, Mengyao Wei, Chaofan Li, Jiawang Qin, Mengjie An, Quanlin Li","doi":"10.1093/hr/uhag080","DOIUrl":"https://doi.org/10.1093/hr/uhag080","url":null,"abstract":"Apple (Malus domestica) is one of the most widely cultivated and consumed fruits worldwide, valued for its rich nutrition and health benefits. Cold limits apple tree growth, development, yield, and fruit quality. Understanding the regulatory networks of apple plants in response to cold stress is crucial for improving their cold tolerance. In this review, we summarize the molecular regulation of apple plants to withstand cold stress involving transcription cascade, hormone signal, reactive oxygen species (ROS) homeostasis, epigenetic control, and post-translational modifications, as well as the crosstalk pathway with drought, immune, and light. We also underscore the management strategies aimed at enhancing apple plants cold tolerance, including the utilization of wild germplasm resources, integration of multi-omics regulatory network, gene editing, molecular marker-assisted breeding, and rootstock grafting. This review provides a molecular basis for gene expression regulation strategies to improve apple trees cold tolerance.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"29 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147360435","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}
Liu Zhenhua, Liang Conglian, Hou Congzhe, Zhang Longfei, Li Jing, Huang Luyao, Zhang Gaixia, Pan Shaobin, Li Runzhu, Liu Chao, Zhang Yongqing, Li Jia, Pu Gaobin
The delayed flower bud opening of Lonicera japonica ‘Huajin 6’ extends its harvest window and enhances agricultural value, yet the underlying molecular basis remains unclear. Here, we assembled a chromosome-level genome of ‘Huajin 6’ using PacBio sequencing and high-throughput chromosome conformation capture (Hi-C) scaffolding (824.72 Mb, scaffold N50 = 91.2 Mb). Comparative genomic analyses revealed a subfamily-specific contraction of lipoxygenase (LOX) genes, particularly within the 9-LOX clade, which is associated with a reduced jasmonate biosynthetic capacity during floral development. Transcriptomic and hormone profiling showed coordinated suppression of jasmonic acid (JA) biosynthesis-related genes and a marked reduction of JA and its bioactive derivatives during the transition from the complete white stage to flower opening. A JA-responsive co-expression module enriched in cell wall modification genes exhibited attenuated activation in ‘Huajin 6’. Functional assays further demonstrated that exogenous JA restored timely flower bud opening in both ‘Huajin 6’ and L. macranthoides, while heterologous expression of Lonicera LOX genes enhanced jasmonate accumulation in Arabidopsis. Together, these findings are consistent with a jasmonate threshold model in which LOX gene contraction constrains JA accumulation during floral transition, contributing to delayed flower bud opening and highlighting how genome structural variation influences hormone-dependent flowering dynamics.
{"title":"Genomic contraction of the LOX gene family limits jasmonic acid biosynthesis and contributes to delayed flower bud opening in honeysuckle ( Lonicera japonica )","authors":"Liu Zhenhua, Liang Conglian, Hou Congzhe, Zhang Longfei, Li Jing, Huang Luyao, Zhang Gaixia, Pan Shaobin, Li Runzhu, Liu Chao, Zhang Yongqing, Li Jia, Pu Gaobin","doi":"10.1093/hr/uhag078","DOIUrl":"https://doi.org/10.1093/hr/uhag078","url":null,"abstract":"The delayed flower bud opening of Lonicera japonica ‘Huajin 6’ extends its harvest window and enhances agricultural value, yet the underlying molecular basis remains unclear. Here, we assembled a chromosome-level genome of ‘Huajin 6’ using PacBio sequencing and high-throughput chromosome conformation capture (Hi-C) scaffolding (824.72 Mb, scaffold N50 = 91.2 Mb). Comparative genomic analyses revealed a subfamily-specific contraction of lipoxygenase (LOX) genes, particularly within the 9-LOX clade, which is associated with a reduced jasmonate biosynthetic capacity during floral development. Transcriptomic and hormone profiling showed coordinated suppression of jasmonic acid (JA) biosynthesis-related genes and a marked reduction of JA and its bioactive derivatives during the transition from the complete white stage to flower opening. A JA-responsive co-expression module enriched in cell wall modification genes exhibited attenuated activation in ‘Huajin 6’. Functional assays further demonstrated that exogenous JA restored timely flower bud opening in both ‘Huajin 6’ and L. macranthoides, while heterologous expression of Lonicera LOX genes enhanced jasmonate accumulation in Arabidopsis. Together, these findings are consistent with a jasmonate threshold model in which LOX gene contraction constrains JA accumulation during floral transition, contributing to delayed flower bud opening and highlighting how genome structural variation influences hormone-dependent flowering dynamics.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"5 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147361009","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}
Hongfei Li, Dongxin Liu, Huailong Teng, Lile Deng, Bo Zheng, Qiang Xu, Shunyuan Xiao, Xiuxin Deng, Zhiyong Pan
Plant growth-promoting rhizobacteria (PGPR) interact with host plants through chemical signals. However, the specific signals in citrus-PGPR interactions remain unclear. Here, we show that a predominant and growth-promoting Burkholderia strain (Burk_2H3) isolated from citrus rhizosphere promotes plant growth by secreting N-(3-oxo-octanoyl)-L-homoserine lactone (PGPHL). Metabolomic analysis revealed that PGPHL abundance in Burk_2H3 secretions was 9.7- to 17.2-fold higher than that in three non-promoting Burkholderia strains. Exogenous application of PGPHL, but not other secretory metabolites, increased citrus seedling dry weight by 43.12%. Transcriptomic analysis showed that Burk_2H3, its cell-free supernatant, or PGPHL consistently upregulated key nutrient transporter genes in roots. Consistently, ionomic analysis confirmed higher root concentrations of nitrogen, phosphorus, and potassium. Field trials further demonstrated that PGPHL increased biomass by 21% in pepper, 15% in celery, and 18% in mustard. Together, these findings identify PGPHL as a candidate for developing plant growth stimulants and biofertilizers.
促进植物生长的根瘤菌（PGPR）通过化学信号与寄主植物相互作用。然而，柑橘- pgpr相互作用中的具体信号仍不清楚。在这里，我们发现从柑橘根际分离的伯克霍尔德菌（Burk_2H3）通过分泌N-（3-氧辛烷基）- l -高丝氨酸内酯（PGPHL）促进植物生长。代谢组学分析显示，Burk_2H3分泌物中的PGPHL丰度比三种非促进型Burkholderia菌株高9.7至17.2倍。外源施用PGPHL可使柑桔幼苗干重增加43.12%，而其他分泌代谢物不加处理。转录组学分析显示，Burk_2H3及其无细胞上清液（PGPHL）持续上调根中关键营养转运基因。与此一致的是，离子分析证实了氮、磷和钾的根浓度较高。田间试验进一步表明，PGPHL使辣椒、芹菜和芥菜的生物量分别增加21%、15%和18%。总之，这些发现确定了PGPHL作为开发植物生长刺激剂和生物肥料的候选物质。
{"title":"Rhizobacteria promote plant growth via secretion of N-(3-Oxooctanoyl)-L-homoserine lactone","authors":"Hongfei Li, Dongxin Liu, Huailong Teng, Lile Deng, Bo Zheng, Qiang Xu, Shunyuan Xiao, Xiuxin Deng, Zhiyong Pan","doi":"10.1093/hr/uhag071","DOIUrl":"https://doi.org/10.1093/hr/uhag071","url":null,"abstract":"Plant growth-promoting rhizobacteria (PGPR) interact with host plants through chemical signals. However, the specific signals in citrus-PGPR interactions remain unclear. Here, we show that a predominant and growth-promoting Burkholderia strain (Burk_2H3) isolated from citrus rhizosphere promotes plant growth by secreting N-(3-oxo-octanoyl)-L-homoserine lactone (PGPHL). Metabolomic analysis revealed that PGPHL abundance in Burk_2H3 secretions was 9.7- to 17.2-fold higher than that in three non-promoting Burkholderia strains. Exogenous application of PGPHL, but not other secretory metabolites, increased citrus seedling dry weight by 43.12%. Transcriptomic analysis showed that Burk_2H3, its cell-free supernatant, or PGPHL consistently upregulated key nutrient transporter genes in roots. Consistently, ionomic analysis confirmed higher root concentrations of nitrogen, phosphorus, and potassium. Field trials further demonstrated that PGPHL increased biomass by 21% in pepper, 15% in celery, and 18% in mustard. Together, these findings identify PGPHL as a candidate for developing plant growth stimulants and biofertilizers.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"23 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147314876","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}
Solanaceous vegetables are continuously threatened by Fusarium wilt disease, which is mainly caused by Fusarium oxysporum (Fo), a fungal species complex comprising many devastating soil-borne pathogens, resulting in severe yield losses worldwide. Over the past decade, significant and numerous advances have been made in dissecting the molecular and genomic basis underlying the interaction between solanaceous vegetables and Fo, particularly owing to the emergence of the tomato-Fo pathosystem as a powerful model system for studying the molecular basis of resistance and susceptibility in solanaceous vegetables against vascular wilt pathogens. In this review, we summarize recent advances driven by improvements in genome sequencing and assembly of Fo infecting solanaceous vegetables, the virulence strategies and diverse arsenals employed by Fo to modulate and suppress host immunity, as well as the identification and functional characterization of race-specific resistance genes in solanaceous vegetables and their corresponding Fo determinants. We address the potential downstream signaling pathways involved in activating solanaceous vegetable immunity against Fo. In addition, we explore emerging insights into microbiome-based strategies for disease control, emphasizing the potential use of beneficial and synthetic microbes in the sustainable management of Fusarium wilt in tomato. Collectively, this review provides an integrated perspective on pathogen genomics, pathogenesis, host resistance, and microbiome-driven control of Fusarium wilt in tomato, offering promising avenues for developing durable and broad-spectrum resistance against various Fo strains in solanaceous vegetables.
{"title":"Solanaceous vegetables and Fusarium oxysporum interactions: pathogen genomics, pathogenesis, host resistance, and emerging microbiome-driven disease management","authors":"Min Li, Lihong Hao, Xinxing Shi, Jianbiao Wang, Haoqian Li, Yifei Wang, Pravin Khambalkar, Xizhe Sun, Sharmin Rima, Xinyi Guo, Xiangling Fang, Lisong Ma","doi":"10.1093/hr/uhag074","DOIUrl":"https://doi.org/10.1093/hr/uhag074","url":null,"abstract":"Solanaceous vegetables are continuously threatened by Fusarium wilt disease, which is mainly caused by Fusarium oxysporum (Fo), a fungal species complex comprising many devastating soil-borne pathogens, resulting in severe yield losses worldwide. Over the past decade, significant and numerous advances have been made in dissecting the molecular and genomic basis underlying the interaction between solanaceous vegetables and Fo, particularly owing to the emergence of the tomato-Fo pathosystem as a powerful model system for studying the molecular basis of resistance and susceptibility in solanaceous vegetables against vascular wilt pathogens. In this review, we summarize recent advances driven by improvements in genome sequencing and assembly of Fo infecting solanaceous vegetables, the virulence strategies and diverse arsenals employed by Fo to modulate and suppress host immunity, as well as the identification and functional characterization of race-specific resistance genes in solanaceous vegetables and their corresponding Fo determinants. We address the potential downstream signaling pathways involved in activating solanaceous vegetable immunity against Fo. In addition, we explore emerging insights into microbiome-based strategies for disease control, emphasizing the potential use of beneficial and synthetic microbes in the sustainable management of Fusarium wilt in tomato. Collectively, this review provides an integrated perspective on pathogen genomics, pathogenesis, host resistance, and microbiome-driven control of Fusarium wilt in tomato, offering promising avenues for developing durable and broad-spectrum resistance against various Fo strains in solanaceous vegetables.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"42 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147361008","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}
Jing Huang, Pei-Xuan Xiao, Ling Cui, Lei Tan, Shenchao Zhu, Junli Ye, Wen-Biao Jiao
Citrus species are economically and nutritionally vital, with their fruits cultivated globally. Despite the publication of multiple genomes for Citrus, high-quality assemblies that achieve both haplotype resolution and telomere-to-telomere (HR-T2T) continuity remain scarce—pummelo (Citrus maxima) being a notable example. Compounded by limitations in gene annotation quality, these gaps hinder functional genomic research and genomics-assisted breeding. Here, we report the first high-quality HR-T2T genome assembly of pummelo, generated using PacBio HiFi and Oxford Nanopore sequencing. The two haplotype assemblies presented contig N50 values of 38.58 Mb and 32.57 Mb, completeness scores of 99.36% and 99.66%, and nucleotide accuracies of 99.99994% and 99.99997%, respectively. We developed HapGene, a haplotype-aware annotation pipeline that integrates short-read RNA-Seq and long-read Iso-Seq data to enable unbiased annotation. Benchmarking showed HapGene captured 3%-10% of genes missed or misannotated by conventional pipelines and reduces false haplotype-specific genes by 4-5-fold. Leveraging 380 Gb of newly sequenced and 2,792 Gb of public transcriptomic data, we comprehensively annotated protein-coding and non-coding genes across three major Citrus crops (sweet orange, pummelo, and mandarin). This effort revealed 18,757-21,083 alternative splicing events, 1,725-1,853 resistance gene analogues, and 2,392-3,757 long intergenic RNAs (lincRNAs). Genomic and transcriptomic characterization of lincRNAs indicated their functional innovation (many associated with stress responses) in Citrus. Additionally, we revealed around one third of genes exhibited tissue-specific allelic differential expression. Our work provides a critical genomic resource and analytical tool to advance Citrus genomic research, thereby driving progress in functional and evolutionary genomics while laying a robust foundation for precise genomics-assisted breeding.
{"title":"Haplotype-resolved telomere-to-telomere assembly and haplotype-aware annotation pipeline enable high-quality reannotation of three Citrus genomes","authors":"Jing Huang, Pei-Xuan Xiao, Ling Cui, Lei Tan, Shenchao Zhu, Junli Ye, Wen-Biao Jiao","doi":"10.1093/hr/uhag048","DOIUrl":"https://doi.org/10.1093/hr/uhag048","url":null,"abstract":"Citrus species are economically and nutritionally vital, with their fruits cultivated globally. Despite the publication of multiple genomes for Citrus, high-quality assemblies that achieve both haplotype resolution and telomere-to-telomere (HR-T2T) continuity remain scarce—pummelo (Citrus maxima) being a notable example. Compounded by limitations in gene annotation quality, these gaps hinder functional genomic research and genomics-assisted breeding. Here, we report the first high-quality HR-T2T genome assembly of pummelo, generated using PacBio HiFi and Oxford Nanopore sequencing. The two haplotype assemblies presented contig N50 values of 38.58 Mb and 32.57 Mb, completeness scores of 99.36% and 99.66%, and nucleotide accuracies of 99.99994% and 99.99997%, respectively. We developed HapGene, a haplotype-aware annotation pipeline that integrates short-read RNA-Seq and long-read Iso-Seq data to enable unbiased annotation. Benchmarking showed HapGene captured 3%-10% of genes missed or misannotated by conventional pipelines and reduces false haplotype-specific genes by 4-5-fold. Leveraging 380 Gb of newly sequenced and 2,792 Gb of public transcriptomic data, we comprehensively annotated protein-coding and non-coding genes across three major Citrus crops (sweet orange, pummelo, and mandarin). This effort revealed 18,757-21,083 alternative splicing events, 1,725-1,853 resistance gene analogues, and 2,392-3,757 long intergenic RNAs (lincRNAs). Genomic and transcriptomic characterization of lincRNAs indicated their functional innovation (many associated with stress responses) in Citrus. Additionally, we revealed around one third of genes exhibited tissue-specific allelic differential expression. Our work provides a critical genomic resource and analytical tool to advance Citrus genomic research, thereby driving progress in functional and evolutionary genomics while laying a robust foundation for precise genomics-assisted breeding.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"25 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147314874","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}
Ethylene and abscisic acid (ABA) play crucial roles in the ripening and softening of persimmon fruit, and they can promote each other to accelerate the softening process. However, the underlying molecular mechanisms remain to be further elucidated. In this study, a transcription factor NAM ATAF1/2, CUC26 (DkNAC26) induced by ethylene was identified. It could increase the content of ABA in persimmon fruit by promoting the expression of ABA synthesis-related gene DkNCED2+3’, thereby reducing fruit firmness. On the other hand, ABA could induce the expression of transcription factor DkNAC28, which binds to the promoter region of the ethylene biosynthesis gene DkACS1, leading to an earlier ethylene burst and consequently accelerating fruit softening. This study elucidates the functional roles of two transcriptional activators, DkNAC26 and DkNAC28, in regulating the biosynthesis of ethylene and ABA and reveals a molecular mechanism through which these two hormones interact to promote fruit softening, providing a new perspective for hormone crosstalk that drives rapid softening in persimmon.
{"title":"ABA–ethylene crosstalk accelerates persimmon fruit softening via induction of DkNAC26 and DkNAC28","authors":"Yaxiu Xu, Fan Yang, Huiru Song, Xinru Zhao, Hui Gao, Ningjing Sun, Xiaofen Liu, Xueren Yin, Yuduan Ding, Qinggang Zhu","doi":"10.1093/hr/uhag055","DOIUrl":"https://doi.org/10.1093/hr/uhag055","url":null,"abstract":"Ethylene and abscisic acid (ABA) play crucial roles in the ripening and softening of persimmon fruit, and they can promote each other to accelerate the softening process. However, the underlying molecular mechanisms remain to be further elucidated. In this study, a transcription factor NAM ATAF1/2, CUC26 (DkNAC26) induced by ethylene was identified. It could increase the content of ABA in persimmon fruit by promoting the expression of ABA synthesis-related gene DkNCED2+3’, thereby reducing fruit firmness. On the other hand, ABA could induce the expression of transcription factor DkNAC28, which binds to the promoter region of the ethylene biosynthesis gene DkACS1, leading to an earlier ethylene burst and consequently accelerating fruit softening. This study elucidates the functional roles of two transcriptional activators, DkNAC26 and DkNAC28, in regulating the biosynthesis of ethylene and ABA and reveals a molecular mechanism through which these two hormones interact to promote fruit softening, providing a new perspective for hormone crosstalk that drives rapid softening in persimmon.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"113 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147314875","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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