Song Gao, Fu Li, Zheng Zeng, Qiaoyun He, Hassan H A Mostafa, Suling Zhang, Taotao Wang, Yanzhou Wang, Touming Liu
The garlic bulb comprises several cloves, the swelling growth of which is significantly hindered by the accumulation of viruses. Herein, we describe a single-cell transcriptomic atlas of swelling cloves with virus accumulation, which comprised 19 681 high-quality cells representing 11 distinct cell clusters. Cells of two clusters, clusters 7 (C7) and 11 (C11), were inferred to be from the meristem. Cell trajectory analysis suggested the differentiation of clove cells to start from the meristem cells, along two pseudo-time paths. Investigation into the cell-specific activity of invasive viruses demonstrated that garlic virus genes showed relatively low expression activity in cells of the clove meristem. There were 2060 garlic genes co-expressed with virus genes, many of which showed an association with the defense response. Five glutathione synthase/reductase genes co-expressed with virus genes displayed up-regulated expression, and the glutathione and related metabolites level showed an alteration in virus-invasive garlic clove, implying the role of glutathione in viral immunity of garlic. Our study offers valuable insights into the clove organogenesis and interaction between garlic and virus at single-cell resolution.
{"title":"A single-cell transcriptomic atlas reveals the cell differentiation trajectory and the response to virus invasion in swelling clove of garlic","authors":"Song Gao, Fu Li, Zheng Zeng, Qiaoyun He, Hassan H A Mostafa, Suling Zhang, Taotao Wang, Yanzhou Wang, Touming Liu","doi":"10.1093/hr/uhae365","DOIUrl":"https://doi.org/10.1093/hr/uhae365","url":null,"abstract":"The garlic bulb comprises several cloves, the swelling growth of which is significantly hindered by the accumulation of viruses. Herein, we describe a single-cell transcriptomic atlas of swelling cloves with virus accumulation, which comprised 19 681 high-quality cells representing 11 distinct cell clusters. Cells of two clusters, clusters 7 (C7) and 11 (C11), were inferred to be from the meristem. Cell trajectory analysis suggested the differentiation of clove cells to start from the meristem cells, along two pseudo-time paths. Investigation into the cell-specific activity of invasive viruses demonstrated that garlic virus genes showed relatively low expression activity in cells of the clove meristem. There were 2060 garlic genes co-expressed with virus genes, many of which showed an association with the defense response. Five glutathione synthase/reductase genes co-expressed with virus genes displayed up-regulated expression, and the glutathione and related metabolites level showed an alteration in virus-invasive garlic clove, implying the role of glutathione in viral immunity of garlic. Our study offers valuable insights into the clove organogenesis and interaction between garlic and virus at single-cell resolution.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"82 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142917752","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}
Yuekun Yang, Shamei Lv, Xiaosan Huang, Ying He, Xiaoyan Zhang, Yu Liu, Guoping Wang, Ni Hong, Liping Wang
Pear ring rot disease (Botryosphaeria dothidea) causes a significant threat to the healthy development of the pear industry. Recent research has identified the functional role of long noncoding RNAs (lncRNAs) in various biological processes of plants. The role of lncRNAs in pear defense response remains unknown. In this study, transcriptome sequencing was used to analyze long non-coding RNAs in pear stem infected with B. dothidea. It showed that 3,555 lncRNAs were identified, of which 286 lncRNAs were significantly differentially expressed. GO and KEGG analysis showed that cis- and trans-regulated target genes were enriched in multiple disease-resistant related pathways. More specifically, MSTRG.32189 predicted as an endogenous target mimic (eTM) was significantly down-regulated in response to B. dothidea infection, which was confirmed to inhibit the cleavage effect of PcmiR399b on PcUBC24. The transgenic Arabidopsis of OE-MSTRG.32189 exhibited lower Pi content and weaker disease resistance to Botrytis cinerea compared to WT. In pear callus, overexpression of MSTRG.32189 negatively regulated PcmiR399b, which decreased Pi content and reduced disease resistance. Whereas overexpressing PcmiR399b in pear callus exhibited the opposite effects compared with OE-MSTRG.32189. Overexpression and knock-out of PcUBC24 further clarified that PcUBC24 negatively regulate the Pi content and disease resistance to B. dothidea infection. Furthermore, the ROS levels and the expressions of disease resistance pathway-related genes were regulated by the MSTRG.32189-PcmiR399b-PcUBC24 module in transgenic pear callus, which contributed to disease resistance. Overall, our results demonstrated the role of lncRNAs in pear defense response, revealing MSTRG.32189-PcmiR399b-PcUBC24 module regulates phosphate accumulation and disease resistance to B. dothidea infection in pear.
{"title":"The long non-coding RNA MSTRG.32189-PcmiR399b-PcUBC24 module regulates the phosphate accumulation and disease resistance to Botryosphaeria dothidea in pear","authors":"Yuekun Yang, Shamei Lv, Xiaosan Huang, Ying He, Xiaoyan Zhang, Yu Liu, Guoping Wang, Ni Hong, Liping Wang","doi":"10.1093/hr/uhae359","DOIUrl":"https://doi.org/10.1093/hr/uhae359","url":null,"abstract":"Pear ring rot disease (Botryosphaeria dothidea) causes a significant threat to the healthy development of the pear industry. Recent research has identified the functional role of long noncoding RNAs (lncRNAs) in various biological processes of plants. The role of lncRNAs in pear defense response remains unknown. In this study, transcriptome sequencing was used to analyze long non-coding RNAs in pear stem infected with B. dothidea. It showed that 3,555 lncRNAs were identified, of which 286 lncRNAs were significantly differentially expressed. GO and KEGG analysis showed that cis- and trans-regulated target genes were enriched in multiple disease-resistant related pathways. More specifically, MSTRG.32189 predicted as an endogenous target mimic (eTM) was significantly down-regulated in response to B. dothidea infection, which was confirmed to inhibit the cleavage effect of PcmiR399b on PcUBC24. The transgenic Arabidopsis of OE-MSTRG.32189 exhibited lower Pi content and weaker disease resistance to Botrytis cinerea compared to WT. In pear callus, overexpression of MSTRG.32189 negatively regulated PcmiR399b, which decreased Pi content and reduced disease resistance. Whereas overexpressing PcmiR399b in pear callus exhibited the opposite effects compared with OE-MSTRG.32189. Overexpression and knock-out of PcUBC24 further clarified that PcUBC24 negatively regulate the Pi content and disease resistance to B. dothidea infection. Furthermore, the ROS levels and the expressions of disease resistance pathway-related genes were regulated by the MSTRG.32189-PcmiR399b-PcUBC24 module in transgenic pear callus, which contributed to disease resistance. Overall, our results demonstrated the role of lncRNAs in pear defense response, revealing MSTRG.32189-PcmiR399b-PcUBC24 module regulates phosphate accumulation and disease resistance to B. dothidea infection in pear.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"25 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142917331","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}
Nitrate (NO3−), a key form of inorganic nitrogen (N) in soils, is typically lost in tea gardens through leaching. However, NO3− utilization efficiency (NiUE) and its characteristic mechanism in tea plants remain unclear. This study screened contrastive genotypes of NiUE using leaf chlorate sensitivity and explored the potential genes that regulate this process. Fresh branches of ten cultivars were hydroponically cultivated and subjected to potassium nitrate (KNO3) and potassium chlorate (KClO3) treatments, with the former as the control group. The sensitive cultivar, Zhenong 117 (ZN117), showed a decrease in SPAD and Fv/Fm values following KClO3 treatment, while the tolerant cultivar, Teiguanyin (TGY), exhibited minimal significant changes. After 5 days of cultivation, the 15N concentration and proportion in new shoots of ZN117 were significantly higher than those in TGY. Transcriptome analysis revealed that the expression of genes responsible for NO3− transport, including the nitrate transporters NRT2.4, NPF4.6, NPF6.1, NPF1.10, and NPF1.11, significantly increased in ZN117 after NO3− supply. Genes involved in NO3− reduction, chlorophyll synthesis, and photosynthesis were progressively induced. Co-expression network analysis indicated that the squamosa promoter binding protein activated the onset of NO3− signaling, while basic helix–loop–helix transcripts were triggered to higher levels during NO3− supply. This study proposes a rapid characterization method of NiUE in woody plants and a speculative molecular regulatory mechanism for the NO3− transfer and remobilization of tea plants. A set of specific genes involved in NO3− transport, reduction, and mobilization were identified and proposed as marker genes for NiUE in tea plants.
{"title":"Characterization of nitrate use efficiency in tea plant (Camellia sinensis) based on leaf chlorate sensitivity","authors":"Wenjing Zhang, Xiaoying Dong, Kang Ni, Lifeng Ma, Lizhi Long, Jianyun Ruan","doi":"10.1093/hr/uhae354","DOIUrl":"https://doi.org/10.1093/hr/uhae354","url":null,"abstract":"Nitrate (NO3−), a key form of inorganic nitrogen (N) in soils, is typically lost in tea gardens through leaching. However, NO3− utilization efficiency (NiUE) and its characteristic mechanism in tea plants remain unclear. This study screened contrastive genotypes of NiUE using leaf chlorate sensitivity and explored the potential genes that regulate this process. Fresh branches of ten cultivars were hydroponically cultivated and subjected to potassium nitrate (KNO3) and potassium chlorate (KClO3) treatments, with the former as the control group. The sensitive cultivar, Zhenong 117 (ZN117), showed a decrease in SPAD and Fv/Fm values following KClO3 treatment, while the tolerant cultivar, Teiguanyin (TGY), exhibited minimal significant changes. After 5 days of cultivation, the 15N concentration and proportion in new shoots of ZN117 were significantly higher than those in TGY. Transcriptome analysis revealed that the expression of genes responsible for NO3− transport, including the nitrate transporters NRT2.4, NPF4.6, NPF6.1, NPF1.10, and NPF1.11, significantly increased in ZN117 after NO3− supply. Genes involved in NO3− reduction, chlorophyll synthesis, and photosynthesis were progressively induced. Co-expression network analysis indicated that the squamosa promoter binding protein activated the onset of NO3− signaling, while basic helix–loop–helix transcripts were triggered to higher levels during NO3− supply. This study proposes a rapid characterization method of NiUE in woody plants and a speculative molecular regulatory mechanism for the NO3− transfer and remobilization of tea plants. A set of specific genes involved in NO3− transport, reduction, and mobilization were identified and proposed as marker genes for NiUE in tea plants.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"26 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142887991","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 CRISPR-Cas9 system can be used to introduce site-specific mutations into the genome of tomato (Solanum lycopersicum) plants. However, the direct application of this revolutionary technology to desirable tomato cultivars has been hindered by the challenges of generating transgenic plants. To address this issue, we developed an efficient and heritable genome editing system using tobacco rattle virus (TRV) for an elite tomato cultivar (the paternal line of Saladette). Notably, this virus-induced genome editing (VIGE) system enables the rapid production of various mutant seeds without the need for additional plant transformation and tissue culture, once a Cas9-expressing tomato line is established. This VIGE system consists of transgenic tomato plants that express Cas9 under the control of the tomato ubiquitin 10 (SlUbi10) gene promoter and a mobile guide RNA scaffold (gRNA:SlmFT) generated using the sequence of the tomato Flowering Locus T (SlFT) gene. We determined its editing efficiency by targeting the tomato phytoene desaturase (SlPDS) gene, which causes photobleaching symptoms when disrupted. Most transgenic seedlings infected with the TRV vectors carrying the SlPDS-targeting sgRNA developed chimeric albino leaves associated with a high frequency of indel mutations in the SlPDS gene. Remarkably, fruits from these plants yielded homozygous SlPDS knockout seeds at rates ranging from 15% to 100%. These results demonstrate the exceptional effectiveness of our VIGE system in rapidly generating heritable genome edits in tomato.
{"title":"Development of an efficient and heritable virus-induced genome editing system in Solanum lycopersicum","authors":"HuiJun Lee, Ji Eun Baik, Kyung-Nam Kim","doi":"10.1093/hr/uhae364","DOIUrl":"https://doi.org/10.1093/hr/uhae364","url":null,"abstract":"The CRISPR-Cas9 system can be used to introduce site-specific mutations into the genome of tomato (Solanum lycopersicum) plants. However, the direct application of this revolutionary technology to desirable tomato cultivars has been hindered by the challenges of generating transgenic plants. To address this issue, we developed an efficient and heritable genome editing system using tobacco rattle virus (TRV) for an elite tomato cultivar (the paternal line of Saladette). Notably, this virus-induced genome editing (VIGE) system enables the rapid production of various mutant seeds without the need for additional plant transformation and tissue culture, once a Cas9-expressing tomato line is established. This VIGE system consists of transgenic tomato plants that express Cas9 under the control of the tomato ubiquitin 10 (SlUbi10) gene promoter and a mobile guide RNA scaffold (gRNA:SlmFT) generated using the sequence of the tomato Flowering Locus T (SlFT) gene. We determined its editing efficiency by targeting the tomato phytoene desaturase (SlPDS) gene, which causes photobleaching symptoms when disrupted. Most transgenic seedlings infected with the TRV vectors carrying the SlPDS-targeting sgRNA developed chimeric albino leaves associated with a high frequency of indel mutations in the SlPDS gene. Remarkably, fruits from these plants yielded homozygous SlPDS knockout seeds at rates ranging from 15% to 100%. These results demonstrate the exceptional effectiveness of our VIGE system in rapidly generating heritable genome edits in tomato.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"335 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142888931","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}
Fungi produce microRNA-like RNAs (milRNAs) with functional importance in various biological processes. Our previous research identified a new milRNA Foc-milR87 from Fusarium oxysporum f. sp. cubense, which contributes to fungal virulence by targeting the pathogen glycosyl hydrolase encoding gene. However, the potential roles of fungal milRNAs in interactions with hosts are not well understood. This study demonstrated that Foc-milR87 specifically suppressed the expression of MaPTI6L, a pathogenesis-related gene that encodes a transcriptional activator in the banana (Musa acuminata Cavendish group cv. ‘Baxi Jiao’) genome, by targeting the 3'untranslated region (UTR) of MaPTI6L. Transient overexpression of MaPTI6L activated plant defense responses that depend on its nuclear localization, yet co-expression with Foc-milR87 attenuated these responses. MaPTI6L enhanced plant resistance by promoting transcription of the salicylic acid (SA) signaling pathway marker gene MaEDS1. Sequence analysis of the MaPTI6L gene in 19 banana varieties, particularly those resistant to Fusarium wilt, uncovered single nucleotide polymorphisms (SNPs) at Foc-milR87 target sites. Experimental validation showed that these SNPs significantly reduce the microRNA's ability to suppress target gene expression. Our findings reveal that Foc-milR87 plays an important role in impairing plant resistance by targeting MaPTI6L mRNA and reducing MaEDS1 transcription during the early infection stage, suggesting the 3'UTR of MaPTI6L as a promising target for genome editing in generation of disease-resistant banana cultivars.
{"title":"A virulent milRNA of Fusarium oxysporum f. sp. cubense impairs plant resistance by targeting banana AP2 transcription factor coding gene MaPTI6L","authors":"Jiaqi Zhong, Junjian Situ, Chengcheng He, Jiahui He, Guanghui Kong, Huaping Li, Zide Jiang, Minhui Li","doi":"10.1093/hr/uhae361","DOIUrl":"https://doi.org/10.1093/hr/uhae361","url":null,"abstract":"Fungi produce microRNA-like RNAs (milRNAs) with functional importance in various biological processes. Our previous research identified a new milRNA Foc-milR87 from Fusarium oxysporum f. sp. cubense, which contributes to fungal virulence by targeting the pathogen glycosyl hydrolase encoding gene. However, the potential roles of fungal milRNAs in interactions with hosts are not well understood. This study demonstrated that Foc-milR87 specifically suppressed the expression of MaPTI6L, a pathogenesis-related gene that encodes a transcriptional activator in the banana (Musa acuminata Cavendish group cv. ‘Baxi Jiao’) genome, by targeting the 3'untranslated region (UTR) of MaPTI6L. Transient overexpression of MaPTI6L activated plant defense responses that depend on its nuclear localization, yet co-expression with Foc-milR87 attenuated these responses. MaPTI6L enhanced plant resistance by promoting transcription of the salicylic acid (SA) signaling pathway marker gene MaEDS1. Sequence analysis of the MaPTI6L gene in 19 banana varieties, particularly those resistant to Fusarium wilt, uncovered single nucleotide polymorphisms (SNPs) at Foc-milR87 target sites. Experimental validation showed that these SNPs significantly reduce the microRNA's ability to suppress target gene expression. Our findings reveal that Foc-milR87 plays an important role in impairing plant resistance by targeting MaPTI6L mRNA and reducing MaEDS1 transcription during the early infection stage, suggesting the 3'UTR of MaPTI6L as a promising target for genome editing in generation of disease-resistant banana cultivars.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"25 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142887992","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}
Qian Tong, Yongjian Wang, Regina Feil, John E Lunn, Xiaobo Xu, Yi Wang, Ghislaine Hilbert-Masson, Junhua Kong, Jinliang Chen, Serge Delrot, Bertrand Beauvoit, Zhenchang Liang, Eric Gomès, Yves Gibon, Zhanwu Dai
High temperatures increase the sugar concentration of grape (Vitis vinifera L.) berries, which can negatively affect the composition and quality of wine, and global climate change is expected to exacerbate this problem. Modifying the source-to-sink ratio of grapevines by selective pruning is a potential strategy to mitigate this. To investigate the effects of low source-to-sink ratio (retaining three leaves per cluster) on carbon metabolism of grape (cv. Cabernet Sauvignon) berries, we conducted an analysis of 42 metabolites, 21 enzyme activities, at nine berry developmental stages，as well as transcriptomes from berries grown under two leaves per cluster. The results revealed that the metabolic pathways were coordinately regulated to maintain homeostasis under low source-to-sink ratio conditions. Because of a delay between metabolites and enzyme activities, the metabolites were loosely correlated with enzyme activities, and a lower density of connectivity between them appeared in low source-to-sink conditions. Otherwise, transcripts of the carbohydrate and amino acid metabolism pathways were enriched by carbon limitation. In summary, this integrated analysis reveals a coordinated regulation of various metabolic pathways that maintains the balance of carbon metabolism and ensures survival in challenging environments, highlighting the high metabolic plasticity of grape berries.
{"title":"Integrated analysis of metabolites and enzyme activities reveals the plasticity of central carbon metabolism in grape (Vitis vinifera cv. Cabernet Sauvignon) berries under carbon limitation","authors":"Qian Tong, Yongjian Wang, Regina Feil, John E Lunn, Xiaobo Xu, Yi Wang, Ghislaine Hilbert-Masson, Junhua Kong, Jinliang Chen, Serge Delrot, Bertrand Beauvoit, Zhenchang Liang, Eric Gomès, Yves Gibon, Zhanwu Dai","doi":"10.1093/hr/uhae363","DOIUrl":"https://doi.org/10.1093/hr/uhae363","url":null,"abstract":"High temperatures increase the sugar concentration of grape (Vitis vinifera L.) berries, which can negatively affect the composition and quality of wine, and global climate change is expected to exacerbate this problem. Modifying the source-to-sink ratio of grapevines by selective pruning is a potential strategy to mitigate this. To investigate the effects of low source-to-sink ratio (retaining three leaves per cluster) on carbon metabolism of grape (cv. Cabernet Sauvignon) berries, we conducted an analysis of 42 metabolites, 21 enzyme activities, at nine berry developmental stages，as well as transcriptomes from berries grown under two leaves per cluster. The results revealed that the metabolic pathways were coordinately regulated to maintain homeostasis under low source-to-sink ratio conditions. Because of a delay between metabolites and enzyme activities, the metabolites were loosely correlated with enzyme activities, and a lower density of connectivity between them appeared in low source-to-sink conditions. Otherwise, transcripts of the carbohydrate and amino acid metabolism pathways were enriched by carbon limitation. In summary, this integrated analysis reveals a coordinated regulation of various metabolic pathways that maintains the balance of carbon metabolism and ensures survival in challenging environments, highlighting the high metabolic plasticity of grape berries.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"13 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142887993","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}
Liubin Wang, Yongxin Wang, Yueqi Wang, Liyun Wu, Mengdi He, Zhuozhuo Mao, Guanhua Liu, Kang Wei, Liyuan Wang
Tea (Camellia sinensis) is widely cultivated throughout the world for its unique flavor and health benefits. Galloylated catechins in tea plants serve as important secondary metabolites that play a pivotal role in tea taste determination and pharmacological effects. However, the genetic basis of galloylated-catechins traits remains elusive. We identified a stable and major-effect quantitative trait locus (QTL) associated with galloylated catechins index (GCI), designated qGCI6.2. Within the QTL’s confidence interval, two shikimate dehydrogenases (CsSDH4, CsSDH3) were identified. These enzymes catalyze gallic acid (GA) production from 3-dehydroquinate dehydratase, thereby contributing to galloylated catechins accumulation. RT-qPCR analysis revealed that CsSDH4 and CsSDH3 expression levels and GA and galloylated catechins contents were positively correlated. Furthermore, overexpressing CsSDH4 and CsSDH3 in transgenic tomato plants markedly increased GA and galloylated catechin contents. RNA-seq analysis of transgenic tomato indicated that CsSDH4 and CsSDH3 primarily regulate genes related to shikimic acid and flavonoid pathways, and jointly promote galloylated catechins synthesis. Our findings have further elucidated the galloylated catechins synthesis pathway and provided a theoretical basis for cultivation of tea cultivars with high galloylated catechin contents.
{"title":"Two shikimate dehydrogenases play an essential role in the biosynthesis of galloylated catechins in tea plants","authors":"Liubin Wang, Yongxin Wang, Yueqi Wang, Liyun Wu, Mengdi He, Zhuozhuo Mao, Guanhua Liu, Kang Wei, Liyuan Wang","doi":"10.1093/hr/uhae356","DOIUrl":"https://doi.org/10.1093/hr/uhae356","url":null,"abstract":"Tea (Camellia sinensis) is widely cultivated throughout the world for its unique flavor and health benefits. Galloylated catechins in tea plants serve as important secondary metabolites that play a pivotal role in tea taste determination and pharmacological effects. However, the genetic basis of galloylated-catechins traits remains elusive. We identified a stable and major-effect quantitative trait locus (QTL) associated with galloylated catechins index (GCI), designated qGCI6.2. Within the QTL’s confidence interval, two shikimate dehydrogenases (CsSDH4, CsSDH3) were identified. These enzymes catalyze gallic acid (GA) production from 3-dehydroquinate dehydratase, thereby contributing to galloylated catechins accumulation. RT-qPCR analysis revealed that CsSDH4 and CsSDH3 expression levels and GA and galloylated catechins contents were positively correlated. Furthermore, overexpressing CsSDH4 and CsSDH3 in transgenic tomato plants markedly increased GA and galloylated catechin contents. RNA-seq analysis of transgenic tomato indicated that CsSDH4 and CsSDH3 primarily regulate genes related to shikimic acid and flavonoid pathways, and jointly promote galloylated catechins synthesis. Our findings have further elucidated the galloylated catechins synthesis pathway and provided a theoretical basis for cultivation of tea cultivars with high galloylated catechin contents.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"24 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142874567","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}
Wenjie Yang, Meng Liu, Landi Feng, Pengfei Jiao, Jiebei Jiang, Li Huang, Jianquan Liu, Jordi Lopez-Pujol, Quanjun Hu
Lobularia maritima (sweet alyssum) is a popular ornamental plant that displays a range of flower colors, particularly white and purple. However, the genetic underpinning and evolutionary history of flower colors have remained unknown. To address this, we performed a de novo assembly of a chromosome-level genome for this species and conducted comparative population genomic analyses of both domestic and wild representatives. These analyses revealed distinct genetic clusters corresponding to wild and domestic groups, with further subdivisions based on geographic and phenotypic differences. Importantly, all cultivars originated from a single domestication event within the Tunisia group. One wild group did not contribute genetically to the current cultivars. The new mutations in key gene of the anthocyanin biosynthetic pathway, PAP1, that arose following domestication led to the origin of purple flower coloration in the cultivars. Moreover, the contrasting PAP1 haplotypes in white and purple varieties lead to differential expression of CHS and DFR, which in turn contributes to the observed flower color differences. These findings provide key insights into the domestication history and genetic regulation of flower color in L. maritima, laying the groundwork for future genetic breeding efforts focused on this plant, especially introducing genetic sources from other wild groups.
{"title":"Domestication history and genetic changes for the newly evolved flower color in the ornamental plant Lobularia maritima (Brassiaceae)","authors":"Wenjie Yang, Meng Liu, Landi Feng, Pengfei Jiao, Jiebei Jiang, Li Huang, Jianquan Liu, Jordi Lopez-Pujol, Quanjun Hu","doi":"10.1093/hr/uhae355","DOIUrl":"https://doi.org/10.1093/hr/uhae355","url":null,"abstract":"Lobularia maritima (sweet alyssum) is a popular ornamental plant that displays a range of flower colors, particularly white and purple. However, the genetic underpinning and evolutionary history of flower colors have remained unknown. To address this, we performed a de novo assembly of a chromosome-level genome for this species and conducted comparative population genomic analyses of both domestic and wild representatives. These analyses revealed distinct genetic clusters corresponding to wild and domestic groups, with further subdivisions based on geographic and phenotypic differences. Importantly, all cultivars originated from a single domestication event within the Tunisia group. One wild group did not contribute genetically to the current cultivars. The new mutations in key gene of the anthocyanin biosynthetic pathway, PAP1, that arose following domestication led to the origin of purple flower coloration in the cultivars. Moreover, the contrasting PAP1 haplotypes in white and purple varieties lead to differential expression of CHS and DFR, which in turn contributes to the observed flower color differences. These findings provide key insights into the domestication history and genetic regulation of flower color in L. maritima, laying the groundwork for future genetic breeding efforts focused on this plant, especially introducing genetic sources from other wild groups.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"14 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142858435","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}
Sen Meng, Na Lian, Fangcuo Qin, Shuqi Yang, Dong Meng, Zhan Bian, Li Xiang, Junkun Lu
Sandalwood (Santalum album), a culturally significant and economically valuable horticultural species, is renowned for its heartwood and essential oils enriched with sesquiterpene compounds such as santalol. Despite progress in elucidating the biosynthetic pathway of these valuable metabolites, the transcriptional regulation of this process, particularly under abiotic stress conditions, remains largely unexplored. Under drought conditions, we observed a marked increase in SaAREB6 expression, paralleled by elevated levels of santalols. Moreover, we identified SaCYP736A167, a cytochrome P450 monooxygenase gene, as a direct target of SaAREB6. Using electrophoretic mobility shift assays (EMSAs), microscale thermophoresis assays (MSTs) and dual luciferase assays (DLAs), we validated the precise and specific interaction of SaAREB6 with the promoter region of SaCYP736A167. This interaction leads to the upregulation of SaCYP736A167, which in turn catalyzes the final steps in the conversion of sesquiterpene precursors to santalols, thereby reinforcing the connection between SaAREB6 activity and increased santalol production during drought. Collectively, our work illuminates the previously uncharacterized role of SaAREB6 in orchestrating a transcriptional regulation that facilitates drought-induced santalol biosynthesis in sandalwood, presenting opportunities for genetic engineering strategies to improve heartwood and essential oil yields in this economically vital species.
{"title":"The AREB transcription factor SaAREB6 promotes drought stress-induced santalol biosynthesis in sandalwood","authors":"Sen Meng, Na Lian, Fangcuo Qin, Shuqi Yang, Dong Meng, Zhan Bian, Li Xiang, Junkun Lu","doi":"10.1093/hr/uhae347","DOIUrl":"https://doi.org/10.1093/hr/uhae347","url":null,"abstract":"Sandalwood (Santalum album), a culturally significant and economically valuable horticultural species, is renowned for its heartwood and essential oils enriched with sesquiterpene compounds such as santalol. Despite progress in elucidating the biosynthetic pathway of these valuable metabolites, the transcriptional regulation of this process, particularly under abiotic stress conditions, remains largely unexplored. Under drought conditions, we observed a marked increase in SaAREB6 expression, paralleled by elevated levels of santalols. Moreover, we identified SaCYP736A167, a cytochrome P450 monooxygenase gene, as a direct target of SaAREB6. Using electrophoretic mobility shift assays (EMSAs), microscale thermophoresis assays (MSTs) and dual luciferase assays (DLAs), we validated the precise and specific interaction of SaAREB6 with the promoter region of SaCYP736A167. This interaction leads to the upregulation of SaCYP736A167, which in turn catalyzes the final steps in the conversion of sesquiterpene precursors to santalols, thereby reinforcing the connection between SaAREB6 activity and increased santalol production during drought. Collectively, our work illuminates the previously uncharacterized role of SaAREB6 in orchestrating a transcriptional regulation that facilitates drought-induced santalol biosynthesis in sandalwood, presenting opportunities for genetic engineering strategies to improve heartwood and essential oil yields in this economically vital species.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"256 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142841512","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}
Acer pentaphyllum Diels (Sapindaceae), a highly threatened maple endemic to the dry-hot valleys of the Yalong River in western Sichuan, China, represents a valuable resource for horticulture and conservation. This study presents the first chromosomal-scale genome assembly of A. pentaphyllum (~626 Mb, 2n = 26), constructed using PacBio HiFi and Hi-C sequencing technologies. Comparative genomic analyses revealed significant recent genomic changes through rapid amplification of transposable elements, particularly long terminal repeat retrotransposons, coinciding with the dramatic climate change during recent uplift of the Hengduan Mountains. Genes involved in photosynthesis, plant hormone signal transduction, and plant-pathogen interaction showed expansion and/or positive selection, potentially reflecting adaptation to the species’ unique dry-hot valley habitat. Population genomic analysis of 227 individuals from 28 populations revealed low genetic diversity (1.04 ± 0.97 × 10-3) compared to other woody species. Phylogeographic patterns suggest an unexpected upstream colonization along the Yalong River, while Quaternary climate fluctuations drove its continuous lineage diversification and population contraction. Assessment of genetic diversity, inbreeding, and genetic load across populations revealed concerning levels of inbreeding and accumulation of deleterious mutations in small, isolated populations, particularly those at range edges (TKX, CDG, TES). Based on these results, we propose conservation strategies, including the identification of management units and recommendations for genetic rescue. These findings not only facilitate the conservation of A. pentaphyllum but also serve as a valuable resource for future horticultural development and as a model for similar studies on other endangered plant species adapted to extreme environments.
{"title":"High-Resolution Genome Assembly and Population Genetic Study of the Endangered Maple Acer pentaphyllum (Sapindaceae): Implications for Conservation Strategies","authors":"Xiong Li, Li-Sha Jiang, Heng-Ning Deng, Qi Yu, Wen-Bin Ju, Xiao-Juan Chen, Yu Feng, Bo Xu","doi":"10.1093/hr/uhae357","DOIUrl":"https://doi.org/10.1093/hr/uhae357","url":null,"abstract":"Acer pentaphyllum Diels (Sapindaceae), a highly threatened maple endemic to the dry-hot valleys of the Yalong River in western Sichuan, China, represents a valuable resource for horticulture and conservation. This study presents the first chromosomal-scale genome assembly of A. pentaphyllum (~626 Mb, 2n = 26), constructed using PacBio HiFi and Hi-C sequencing technologies. Comparative genomic analyses revealed significant recent genomic changes through rapid amplification of transposable elements, particularly long terminal repeat retrotransposons, coinciding with the dramatic climate change during recent uplift of the Hengduan Mountains. Genes involved in photosynthesis, plant hormone signal transduction, and plant-pathogen interaction showed expansion and/or positive selection, potentially reflecting adaptation to the species’ unique dry-hot valley habitat. Population genomic analysis of 227 individuals from 28 populations revealed low genetic diversity (1.04 ± 0.97 × 10-3) compared to other woody species. Phylogeographic patterns suggest an unexpected upstream colonization along the Yalong River, while Quaternary climate fluctuations drove its continuous lineage diversification and population contraction. Assessment of genetic diversity, inbreeding, and genetic load across populations revealed concerning levels of inbreeding and accumulation of deleterious mutations in small, isolated populations, particularly those at range edges (TKX, CDG, TES). Based on these results, we propose conservation strategies, including the identification of management units and recommendations for genetic rescue. These findings not only facilitate the conservation of A. pentaphyllum but also serve as a valuable resource for future horticultural development and as a model for similar studies on other endangered plant species adapted to extreme environments.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"697 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142841509","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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