Songchong Lu, Yan Sun, Xinshuang Zhang, Wenying Zhu, Xin Liu, Fu Wang, Sheng Luan, Aoxue Wang, Hui Wang
Soil salinization poses a serious threat to plant development and represents a major obstacle to the sustainable production of crops worldwide. Melatonin (MT) contributes prominently to plant tolerance against abiotic environments. However, the molecular basis of transcriptional regulation underlying melatonin accumulation in tomato under saline-alkali stress is still largely unknown. Herein, we identify SlNAC2, a NAC transcription factor in tomato induced by saline–alkali stress, which suppresses the key melatonin biosynthetic genes SlCOMT2 and SlSNAT, while activating SlCV, a gene linked to ROS accumulation and programmed cell death. These regulatory effects reduce MT levels and promote excessive ROS production, ultimately altering the plant’s tolerance to saline–alkali stress. Silencing of SlNAC2 through RNA interference method significantly improves saline-alkali tolerance in tomato, while its constitutive overexpression shows increased susceptibility to saline–alkali stress. Further evidence reveals that under saline-alkali conditions, SlNAC2 directly targets cis-elements of SlCOMT2 and SlSNAT promoters, suppressing their transcription and consequently reducing melatonin levels, whereas simultaneously binding to the SlCV promoter to activate its expression, ultimately leading to ROS accumulation. Moreover, comprehensive protein interaction analyses confirmed that SlNAC2 physically associates with SlDREB2, a DREB-type transcription factor involved in salt stress response. Through its interaction with SlNAC2, SlDREB2 partially attenuates its repression of SlCOMT2 and SlSNAT, thereby increasing melatonin accumulation and ROS scavenging, ultimately enhancing tomato’s resilience to saline–alkali stress conditions. Collectively, our findings reveal a SlNAC2–SlDREB2 regulatory module that finely tunes melatonin synthesis and ROS levels to regulate tomato’s response to saline–alkali stress, providing new strategies for developing stress-resilient tomato varieties.
{"title":"Tomato NAC2-DREB2 module fine-tunes saline-alkali stress sensitivity via modulation of melatonin biosynthesis and ROS homeostasis","authors":"Songchong Lu, Yan Sun, Xinshuang Zhang, Wenying Zhu, Xin Liu, Fu Wang, Sheng Luan, Aoxue Wang, Hui Wang","doi":"10.1093/hr/uhag029","DOIUrl":"https://doi.org/10.1093/hr/uhag029","url":null,"abstract":"Soil salinization poses a serious threat to plant development and represents a major obstacle to the sustainable production of crops worldwide. Melatonin (MT) contributes prominently to plant tolerance against abiotic environments. However, the molecular basis of transcriptional regulation underlying melatonin accumulation in tomato under saline-alkali stress is still largely unknown. Herein, we identify SlNAC2, a NAC transcription factor in tomato induced by saline–alkali stress, which suppresses the key melatonin biosynthetic genes SlCOMT2 and SlSNAT, while activating SlCV, a gene linked to ROS accumulation and programmed cell death. These regulatory effects reduce MT levels and promote excessive ROS production, ultimately altering the plant’s tolerance to saline–alkali stress. Silencing of SlNAC2 through RNA interference method significantly improves saline-alkali tolerance in tomato, while its constitutive overexpression shows increased susceptibility to saline–alkali stress. Further evidence reveals that under saline-alkali conditions, SlNAC2 directly targets cis-elements of SlCOMT2 and SlSNAT promoters, suppressing their transcription and consequently reducing melatonin levels, whereas simultaneously binding to the SlCV promoter to activate its expression, ultimately leading to ROS accumulation. Moreover, comprehensive protein interaction analyses confirmed that SlNAC2 physically associates with SlDREB2, a DREB-type transcription factor involved in salt stress response. Through its interaction with SlNAC2, SlDREB2 partially attenuates its repression of SlCOMT2 and SlSNAT, thereby increasing melatonin accumulation and ROS scavenging, ultimately enhancing tomato’s resilience to saline–alkali stress conditions. Collectively, our findings reveal a SlNAC2–SlDREB2 regulatory module that finely tunes melatonin synthesis and ROS levels to regulate tomato’s response to saline–alkali stress, providing new strategies for developing stress-resilient tomato varieties.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"7 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146071533","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}
Xueying Zhang, Chaomin Chen, Linying Li, Yuqing He, Qinhua Lu, Da Li, Xuanyu He, Qingsheng Li, Gaojie Hong
Anthracnose, caused by Colletotrichum species, poses a significant threat to global tea (Camellia sinensis) production, yet its inducible resistance mechanisms remain largely uncharacterized. Through integrated transcriptomic and metabolomic analyses of the anthracnose-resistant cultivar ‘Zijuan’ and the susceptible cultivar ‘Longjing43’, we identified sakuranetin as a key phytoalexin in tea plants and elucidated a complete jasmonic acid (JA)-mediated defense pathway. Our functional characterization revealed that CsNOMT (Cha09g008790), a naringenin 7-O-methyltransferase, catalyzes sakuranetin biosynthesis with high substrate specificity. Following infection with Colletotrichum camelliae, sakuranetin accumulated exclusively in resistant cultivars, exhibiting superior antifungal activity compared to major tea catechins. Functional validation demonstrated that overexpression of CsNOMT enhanced both sakuranetin accumulation and disease resistance, while gene silencing compromised both traits. Mechanistically, we established that the JA-responsive transcription factor CsMYC2.1 directly activates CsNOMT transcription via G-box binding, establishing a novel JA-CsMYC2.1-CsNOMT-sakuranetin defense axis that distinguishes resistant from susceptible tea cultivars. This study represents the first comprehensive characterization of inducible phytoalexin-mediated immunity in tea, providing immediate applications for sustainable tea production. CsNOMT serves as a valuable functional marker for resistance breeding, while sakuranetin emerges as a promising natural biopesticide to reduce reliance on synthetic fungicides.
{"title":"The JA-CsMYC2.1-CsNOMT-Sakuranetin module contributes to differential anthracnose resistance in Camellia sinensis","authors":"Xueying Zhang, Chaomin Chen, Linying Li, Yuqing He, Qinhua Lu, Da Li, Xuanyu He, Qingsheng Li, Gaojie Hong","doi":"10.1093/hr/uhag022","DOIUrl":"https://doi.org/10.1093/hr/uhag022","url":null,"abstract":"Anthracnose, caused by Colletotrichum species, poses a significant threat to global tea (Camellia sinensis) production, yet its inducible resistance mechanisms remain largely uncharacterized. Through integrated transcriptomic and metabolomic analyses of the anthracnose-resistant cultivar ‘Zijuan’ and the susceptible cultivar ‘Longjing43’, we identified sakuranetin as a key phytoalexin in tea plants and elucidated a complete jasmonic acid (JA)-mediated defense pathway. Our functional characterization revealed that CsNOMT (Cha09g008790), a naringenin 7-O-methyltransferase, catalyzes sakuranetin biosynthesis with high substrate specificity. Following infection with Colletotrichum camelliae, sakuranetin accumulated exclusively in resistant cultivars, exhibiting superior antifungal activity compared to major tea catechins. Functional validation demonstrated that overexpression of CsNOMT enhanced both sakuranetin accumulation and disease resistance, while gene silencing compromised both traits. Mechanistically, we established that the JA-responsive transcription factor CsMYC2.1 directly activates CsNOMT transcription via G-box binding, establishing a novel JA-CsMYC2.1-CsNOMT-sakuranetin defense axis that distinguishes resistant from susceptible tea cultivars. This study represents the first comprehensive characterization of inducible phytoalexin-mediated immunity in tea, providing immediate applications for sustainable tea production. CsNOMT serves as a valuable functional marker for resistance breeding, while sakuranetin emerges as a promising natural biopesticide to reduce reliance on synthetic fungicides.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"76 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146071600","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 transcription factor BRASSINAZOLE-RESISTANT 1 (BZR1) plays a crucial role not only in plant responses to various biotic and abiotic stresses but also serves a critical function in plant growth and development. In this study, we analyzed the origin and evolution of the BZR family in plants. Then, we identified 9 CaBZR1 genes from the pepper pan-genome and performed bioinformatics analyses. Through the integration of transcriptome data analysis with our prior bioinformatics findings, we have identified and selected a specific member of the CaBZR1 family, CaBZR1.2, for further comprehensive investigation. We systematically investigated the biological function of CaBZR1.2 in pepper through classical reverse genetics approaches and subsequently identified proteins that interact with CaBZR1.2. After inhibiting the expression of CaBZR1.2 via the virus-induced gene silencing (VIGS), the growth of pepper lateral branches was significantly suppressed, whereas heterologous overexpression of CaBZR1.2 increased lateral branch number in tomato. This result confirms the key role of CaBZR1.2 in the development of pepper lateral branches. Furthermore, protein-protein interaction assays confirmed that the Sucrose Non-fermenting 1-Related Protein Kinase 1 β subunit 2 (CaSnRK1β2) protein interacts with CaBZR1.2, with subsequent analyses revealing that these two proteins modulate pepper lateral branch development through a mutually antagonistic regulatory mechanism. This study reveals a novel mechanism by which CaBZR1.2 and CaSnRK1β2 coordinately regulate lateral branch development in pepper, providing candidate genes and a theoretical basis for the molecular breeding of pepper plant architecture.
{"title":"Origin and evolution of BZR gene family in plants, pan-genome analysis of the BZR1 gene family and functional characterization of CaBZR1.2 in pepper lateral branch development","authors":"Wujun Xing, Dan Zhang, Peiru Li, Qingzhi Cui, Xinyi Huang, Lianzhen Mao, Yanan Zhao, Jingwei Duan, Yanlong Li, Sha Yang, Cheng Xiong, Xuexiao Zou, Xiongze Dai, Lijun Ou, Zhoubin Liu","doi":"10.1093/hr/uhag015","DOIUrl":"https://doi.org/10.1093/hr/uhag015","url":null,"abstract":"The transcription factor BRASSINAZOLE-RESISTANT 1 (BZR1) plays a crucial role not only in plant responses to various biotic and abiotic stresses but also serves a critical function in plant growth and development. In this study, we analyzed the origin and evolution of the BZR family in plants. Then, we identified 9 CaBZR1 genes from the pepper pan-genome and performed bioinformatics analyses. Through the integration of transcriptome data analysis with our prior bioinformatics findings, we have identified and selected a specific member of the CaBZR1 family, CaBZR1.2, for further comprehensive investigation. We systematically investigated the biological function of CaBZR1.2 in pepper through classical reverse genetics approaches and subsequently identified proteins that interact with CaBZR1.2. After inhibiting the expression of CaBZR1.2 via the virus-induced gene silencing (VIGS), the growth of pepper lateral branches was significantly suppressed, whereas heterologous overexpression of CaBZR1.2 increased lateral branch number in tomato. This result confirms the key role of CaBZR1.2 in the development of pepper lateral branches. Furthermore, protein-protein interaction assays confirmed that the Sucrose Non-fermenting 1-Related Protein Kinase 1 β subunit 2 (CaSnRK1β2) protein interacts with CaBZR1.2, with subsequent analyses revealing that these two proteins modulate pepper lateral branch development through a mutually antagonistic regulatory mechanism. This study reveals a novel mechanism by which CaBZR1.2 and CaSnRK1β2 coordinately regulate lateral branch development in pepper, providing candidate genes and a theoretical basis for the molecular breeding of pepper plant architecture.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"30 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146005983","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}
Ana M González, Ana M Pesqueira, Rocío Fonseca, Sandra Bretones, Fernando J Yuste-Lisbona, Rafael Lozano, Marta Santalla
Flowering time is a critical trait in common bean (Phaseolus vulgaris), influencing yield stability and geographical adaptation. While PvCOL2 and PvPHYA3 are known regulators under long-day (LD) conditions, we identified a third major locus through fine-mapping of the QTL DTF9.4/DTF9.5. Within this region, PvE1 (Phvul.009G204600) emerged as a strong candidate, sharing sequence homology with the soybean E1 gene and acting as a transcriptional repressor of flowering. A naturally occurring 34-bp deletion in its 3′ UTR (e1-del) was associated with early flowering and reduced photoperiod sensitivity. Expression analysis revealed that PvE1 displays a circadian rhythm under LD conditions, with a bimodal pattern peaking in the morning and early evening, resembling that reported for soybean E1. Phenotypic analyses of near-isogenic lines (NILs) confirmed that PvE1 delays flowering specifically under LD and also influences plant architecture, as e1 genotypes exhibited reduced plant height and node number. Functional dissection revealed that PvE1 and PvCOL2 act in partially redundant pathways to repress PvFT gene expression, with evidence of functional interaction. This regulatory module resembles that in soybean but shows species-specific divergence likely shaped by separate evolutionary paths. Genetic diversity analysis identified two rare PvE1 alleles, e1-del and e1-fs, both associated with earlier flowering when combined with col2 mutations, indicating additive effects and reduced photoperiod sensitivity. Although functional validation by transformation was not performed, the use of NILs provides robust genetic evidence of PvE1 activity. Together, these findings establish PvE1 as a conserved legume-specific floral repressor in common bean, with novel allelic variants that can be exploited to develop early-flowering, photoperiod-insensitive cultivars adapted to temperate and high-latitude regions.
{"title":"PvE1 plays an essential role in regulating photoperiod sensitivity and flowering time in common bean","authors":"Ana M González, Ana M Pesqueira, Rocío Fonseca, Sandra Bretones, Fernando J Yuste-Lisbona, Rafael Lozano, Marta Santalla","doi":"10.1093/hr/uhag021","DOIUrl":"https://doi.org/10.1093/hr/uhag021","url":null,"abstract":"Flowering time is a critical trait in common bean (Phaseolus vulgaris), influencing yield stability and geographical adaptation. While PvCOL2 and PvPHYA3 are known regulators under long-day (LD) conditions, we identified a third major locus through fine-mapping of the QTL DTF9.4/DTF9.5. Within this region, PvE1 (Phvul.009G204600) emerged as a strong candidate, sharing sequence homology with the soybean E1 gene and acting as a transcriptional repressor of flowering. A naturally occurring 34-bp deletion in its 3′ UTR (e1-del) was associated with early flowering and reduced photoperiod sensitivity. Expression analysis revealed that PvE1 displays a circadian rhythm under LD conditions, with a bimodal pattern peaking in the morning and early evening, resembling that reported for soybean E1. Phenotypic analyses of near-isogenic lines (NILs) confirmed that PvE1 delays flowering specifically under LD and also influences plant architecture, as e1 genotypes exhibited reduced plant height and node number. Functional dissection revealed that PvE1 and PvCOL2 act in partially redundant pathways to repress PvFT gene expression, with evidence of functional interaction. This regulatory module resembles that in soybean but shows species-specific divergence likely shaped by separate evolutionary paths. Genetic diversity analysis identified two rare PvE1 alleles, e1-del and e1-fs, both associated with earlier flowering when combined with col2 mutations, indicating additive effects and reduced photoperiod sensitivity. Although functional validation by transformation was not performed, the use of NILs provides robust genetic evidence of PvE1 activity. Together, these findings establish PvE1 as a conserved legume-specific floral repressor in common bean, with novel allelic variants that can be exploited to develop early-flowering, photoperiod-insensitive cultivars adapted to temperate and high-latitude regions.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"87 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146022177","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}
Xingnuo Li, Aidi Zhang, Muqaddas Bano, Juan Jin, Qing Hao, Dingyu Fan, Liang Chen, Xiujun Zhang
Jujube (Ziziphus jujuba Mill.) is a fruit crop of high economic value, renowned for its distinctive flavor and wide range of phenotypic diversity. Despite major advancements in jujube genomics, the role of genetic variants in underlying agronomic trait formation is still poorly understood. Here, we used seven high quality jujube genomes to construct a pan-TE (transposon element) map and investigated how TEs shape genome evolution and agronomic traits. We found that TEs constitute 29.05–30.38% of the genome, predominantly long terminal repeat (LTR) retrotransposons such as Copia and Gypsy. A positive correlation (R2 = 0.76) between TE content and genome size underscores their role in genomic expansion. TE insertions within gene bodies significantly reduce gene expression, particularly for genes involved in cell wall biosynthesis and glucose metabolism. Population scale analysis of 1041 accessions identified 4176 TIPs that distinguish wild and cultivated groups. Wild jujubes harbor stress related TIPs (e.g., in peroxidase genes), whereas cultivated accessions carry TIPs linked to fruit development. Notably, a Gypsy insertion upstream of the cellulose synthase gene ZjCESA4 is associated with reduced expression and thinner pericarp in ‘Dongzao’ compared to ‘Huizao.’ Similarly, a downstream LTR/Gypsy insertion near the MADS-box transcription factor gene ZjAGL18 correlates with suppressed expression, highlighting the recurrent targeting of key regulatory genes by TEs during domestication. Our findings demonstrate that TIPs are a major source of genetic variation in jujube, providing molecular markers for breeding programs that aim to balance fruit quality and stress resilience.
{"title":"The jujube pan-TE map identifies transposable element insertions associated with domestication and pericarp development","authors":"Xingnuo Li, Aidi Zhang, Muqaddas Bano, Juan Jin, Qing Hao, Dingyu Fan, Liang Chen, Xiujun Zhang","doi":"10.1093/hr/uhaf343","DOIUrl":"https://doi.org/10.1093/hr/uhaf343","url":null,"abstract":"Jujube (Ziziphus jujuba Mill.) is a fruit crop of high economic value, renowned for its distinctive flavor and wide range of phenotypic diversity. Despite major advancements in jujube genomics, the role of genetic variants in underlying agronomic trait formation is still poorly understood. Here, we used seven high quality jujube genomes to construct a pan-TE (transposon element) map and investigated how TEs shape genome evolution and agronomic traits. We found that TEs constitute 29.05–30.38% of the genome, predominantly long terminal repeat (LTR) retrotransposons such as Copia and Gypsy. A positive correlation (R2 = 0.76) between TE content and genome size underscores their role in genomic expansion. TE insertions within gene bodies significantly reduce gene expression, particularly for genes involved in cell wall biosynthesis and glucose metabolism. Population scale analysis of 1041 accessions identified 4176 TIPs that distinguish wild and cultivated groups. Wild jujubes harbor stress related TIPs (e.g., in peroxidase genes), whereas cultivated accessions carry TIPs linked to fruit development. Notably, a Gypsy insertion upstream of the cellulose synthase gene ZjCESA4 is associated with reduced expression and thinner pericarp in ‘Dongzao’ compared to ‘Huizao.’ Similarly, a downstream LTR/Gypsy insertion near the MADS-box transcription factor gene ZjAGL18 correlates with suppressed expression, highlighting the recurrent targeting of key regulatory genes by TEs during domestication. Our findings demonstrate that TIPs are a major source of genetic variation in jujube, providing molecular markers for breeding programs that aim to balance fruit quality and stress resilience.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"187 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146005982","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}
Somatic embryogenesis is a crucial biotechnological approach for effectively addressing garlic variety degeneration and improving yield and quality. Previous studies have demonstrated that the long non-coding RNA 125175 (lncRNA125175) is specifically induced and expressed during somatic embryogenesis, and may act as an endogenous target mimic (eTM) of AsmiR393h to participate in the regulation of somatic embryogenesis. On this basis, the present study systematically elucidated the functions of the lncRNA125175/AsmiR393h/AsTIR1 regulatory module and its upstream transcriptional mechanism. First, transient expression assays in tobacco leaves and protoplast experiments in garlic suggested that lncRNA125175 served as a competing endogenous RNA (ceRNA) to sequester AsmiR393h, thereby attenuating its post-transcriptional cleavage of the target gene AsTIR1. Promoter analysis revealed that all core components of this module contain auxin cis-acting elements, and the promoter activities of lncRNA125175 and AsTIR1 are significantly induced by exogenous auxin, suggesting that this ceRNA network is precisely regulated by auxin signaling. Further weighted gene co-expression network analysis (WGCNA) identified the auxin response factor AsARF16 as a key upstream regulator. Yeast one-hybrid and two-hybrid assays indicated that AsARF16 can directly bind to the promoter of lncRNA125175, and interact with the transcription factor AsWRKY31 and the auxin signaling factor AsIAA33 to form a transcriptional activation complex. In conclusion, this study uncovers a cascade pathway from auxin signal perception (the AsARF16 complex) to transcriptional activation (lncRNA125175), followed by post-transcriptional ceRNA regulation. It systematically clarifies the molecular mechanism underlying its precise regulation of garlic somatic embryogenesis, providing critical theoretical basis for the targeted improvement of garlic regeneration efficiency and genetic transformation systems.
{"title":"Auxin-Induced AsARF16 Complex Orchestrates lncRNA125175-Mediated ceRNA Networks to Regulate Garlic Somatic Embryogenesis","authors":"Yunhe Bai, Jiaojiao Ruan, Fangling Jiang, Fei Ding, Yuqing Cui, Min Liu, Ping Li, Meng Zhang, Mengqian Li, Hanyu Wei, Rong Zhou, Zhen Wu","doi":"10.1093/hr/uhag016","DOIUrl":"https://doi.org/10.1093/hr/uhag016","url":null,"abstract":"Somatic embryogenesis is a crucial biotechnological approach for effectively addressing garlic variety degeneration and improving yield and quality. Previous studies have demonstrated that the long non-coding RNA 125175 (lncRNA125175) is specifically induced and expressed during somatic embryogenesis, and may act as an endogenous target mimic (eTM) of AsmiR393h to participate in the regulation of somatic embryogenesis. On this basis, the present study systematically elucidated the functions of the lncRNA125175/AsmiR393h/AsTIR1 regulatory module and its upstream transcriptional mechanism. First, transient expression assays in tobacco leaves and protoplast experiments in garlic suggested that lncRNA125175 served as a competing endogenous RNA (ceRNA) to sequester AsmiR393h, thereby attenuating its post-transcriptional cleavage of the target gene AsTIR1. Promoter analysis revealed that all core components of this module contain auxin cis-acting elements, and the promoter activities of lncRNA125175 and AsTIR1 are significantly induced by exogenous auxin, suggesting that this ceRNA network is precisely regulated by auxin signaling. Further weighted gene co-expression network analysis (WGCNA) identified the auxin response factor AsARF16 as a key upstream regulator. Yeast one-hybrid and two-hybrid assays indicated that AsARF16 can directly bind to the promoter of lncRNA125175, and interact with the transcription factor AsWRKY31 and the auxin signaling factor AsIAA33 to form a transcriptional activation complex. In conclusion, this study uncovers a cascade pathway from auxin signal perception (the AsARF16 complex) to transcriptional activation (lncRNA125175), followed by post-transcriptional ceRNA regulation. It systematically clarifies the molecular mechanism underlying its precise regulation of garlic somatic embryogenesis, providing critical theoretical basis for the targeted improvement of garlic regeneration efficiency and genetic transformation systems.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"63 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146006260","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}
Although triploid poplars have larger cells and leaves than their diploid counterparts, the molecular mechanisms underlying this disparity remain elusive. Here, we found that PpnGATA8 and PpnGRF5 were significantly up-regulated in triploid poplars through differential gene expression analysis between diploid and triploid poplars. Furthermore, through genetic transformation in poplar, it was found that both PpnGATA8 and PpnGRF5 positively regulated poplar cell size, resulting in increased leaf size and improved photosynthetic efficiency. RNA-sequencing of PpnGATA8-overexpressing poplars showed that PpnGATA8 promotes expression of PagGRF5 and PagXTH9. Yeast one-hybrid system, electrophoretic mobility shift assay, and dual-luciferase assay were employed to substantiate that PpnGATA8 directly regulated PagGRF5 and PagXTH9 expression. Meanwhile, PpnGRF5 positively regulates the expression of PagXTH9. Poplar protoplast co-transformation assays further proved that co-expression of PpnGATA8 and PpnGRF5 had the strongest effect on promoting PagXTH9 expression. Moreover, overexpression of PpnXTH9 also significantly increased poplar cell and leaf size. Therefore, GATA8, GRF5 and XTH9 formed a feed-forward regulatory loop to regulate plant cell size. Our results are of major significance for revealing the molecular regulatory mechanisms of plant cell size and leaf development, especially the genetic basis of giant variation in cells and leaves in polyploid plants.
{"title":"The GATA8-GRF5-XTH9 feed-forward loop regulates cell size in poplar","authors":"Yufei Xia, Wenqi Wu, Aoyu Ling, Shenxiu Jiang, Jianghai Shu, Shun Wang, Xinli Xia, Xiangyang Kang","doi":"10.1093/hr/uhag019","DOIUrl":"https://doi.org/10.1093/hr/uhag019","url":null,"abstract":"Although triploid poplars have larger cells and leaves than their diploid counterparts, the molecular mechanisms underlying this disparity remain elusive. Here, we found that PpnGATA8 and PpnGRF5 were significantly up-regulated in triploid poplars through differential gene expression analysis between diploid and triploid poplars. Furthermore, through genetic transformation in poplar, it was found that both PpnGATA8 and PpnGRF5 positively regulated poplar cell size, resulting in increased leaf size and improved photosynthetic efficiency. RNA-sequencing of PpnGATA8-overexpressing poplars showed that PpnGATA8 promotes expression of PagGRF5 and PagXTH9. Yeast one-hybrid system, electrophoretic mobility shift assay, and dual-luciferase assay were employed to substantiate that PpnGATA8 directly regulated PagGRF5 and PagXTH9 expression. Meanwhile, PpnGRF5 positively regulates the expression of PagXTH9. Poplar protoplast co-transformation assays further proved that co-expression of PpnGATA8 and PpnGRF5 had the strongest effect on promoting PagXTH9 expression. Moreover, overexpression of PpnXTH9 also significantly increased poplar cell and leaf size. Therefore, GATA8, GRF5 and XTH9 formed a feed-forward regulatory loop to regulate plant cell size. Our results are of major significance for revealing the molecular regulatory mechanisms of plant cell size and leaf development, especially the genetic basis of giant variation in cells and leaves in polyploid plants.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"58 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146005984","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}
Senlin Zeng, Juan Du, Xudong Sun, Lamei Zheng, Xu Li, Sodmergen Sodmergen, Kunzhi Li, Huini Xu
DNA-binding with one finger (DOF) proteins are plant-specific transcription factors (TFs) that play critical roles in plant growth and development, including nitrogen metabolism, but the roles of these TFs in the nitrogen response of tomato (Solanum lycopersicum) remain largely unexplored. Here, we show that overexpressing the DOF gene SlDOF3.4 enhanced the growth of tomato seedlings under low nitrogen (LN) conditions, resulting in longer roots and greater biomass accumulation. Multiple assays demonstrated that SlDOF3.4 interacts with another DOF family member, SlCDF4, and that both TFs bind to the promoters of the N-assimilation gene Glutamine synthetase (SlGS) and the jasmonic acid (JA) biosynthesis gene Lipoxygenase (SlLOXD), suggesting that SlDOF3.4 and SlCDF4 cooperatively regulate nitrogen assimilation and JA biosynthesis. In support of this notion, co-expressing SlCDF4 and SlDOF3.4 enhanced the binding activity of SlDOF3.4 to the SlGS and SlLOXD promoters in a dual-luciferase reporter assay. Under LN conditions, genes related to nitrogen assimilation and JA biosynthesis were markedly upregulated in SlDOF3.4-overexpressing and SlCDF4-overexpressing tomato plants. Knockout of SlCDF4 impaired plant growth under LN conditions, a phenotype that was partially alleviated by treatment with methyl jasmonate. These results provide insight into the roles of DOF TFs in nitrogen assimilation and JA biosynthesis in crops.
{"title":"The SlDOF3.4-SlCDF4 module improves tomato growth under low-nitrogen conditions","authors":"Senlin Zeng, Juan Du, Xudong Sun, Lamei Zheng, Xu Li, Sodmergen Sodmergen, Kunzhi Li, Huini Xu","doi":"10.1093/hr/uhag020","DOIUrl":"https://doi.org/10.1093/hr/uhag020","url":null,"abstract":"DNA-binding with one finger (DOF) proteins are plant-specific transcription factors (TFs) that play critical roles in plant growth and development, including nitrogen metabolism, but the roles of these TFs in the nitrogen response of tomato (Solanum lycopersicum) remain largely unexplored. Here, we show that overexpressing the DOF gene SlDOF3.4 enhanced the growth of tomato seedlings under low nitrogen (LN) conditions, resulting in longer roots and greater biomass accumulation. Multiple assays demonstrated that SlDOF3.4 interacts with another DOF family member, SlCDF4, and that both TFs bind to the promoters of the N-assimilation gene Glutamine synthetase (SlGS) and the jasmonic acid (JA) biosynthesis gene Lipoxygenase (SlLOXD), suggesting that SlDOF3.4 and SlCDF4 cooperatively regulate nitrogen assimilation and JA biosynthesis. In support of this notion, co-expressing SlCDF4 and SlDOF3.4 enhanced the binding activity of SlDOF3.4 to the SlGS and SlLOXD promoters in a dual-luciferase reporter assay. Under LN conditions, genes related to nitrogen assimilation and JA biosynthesis were markedly upregulated in SlDOF3.4-overexpressing and SlCDF4-overexpressing tomato plants. Knockout of SlCDF4 impaired plant growth under LN conditions, a phenotype that was partially alleviated by treatment with methyl jasmonate. These results provide insight into the roles of DOF TFs in nitrogen assimilation and JA biosynthesis in crops.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"88 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146006261","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}
N Pavani, K S Shivashankara, N R Prasannakumar, D C Lakshmana Reddy, P D Kamala Jayanthi, R P Vasanthi, M Reddi Sekhar, Naresh Ponnam, K Madhavi Reddy
Chilli incurs substantial yield losses due to Thrips parvispinus (Karny) infestation, necessitating sustainable resistance breeding strategies. Understanding biochemical basis of resistance will help in exploring the candidate metabolites for indirect selection. LC-MS and GC-MS profiling of two resistant (IIHR-B-HP-79, IIHR 4550) and two susceptible (IIHR 3455, IIHR 4604) chilli accessions were performed. LC-MS profiling revealed Inositol with higher levels in susceptible accession IIHR 3455 (8.74μg/g & 0.33μg/g; VIP score: 2 & 2.5 under control and infested conditions respectively), indicating its role as a stress-induced metabolite rather than a marker for resistance. Secondary metabolites contribution to resistance was genotype-specific and may possibly be driven by complex interactions among these metabolites. Untargeted leaf volatile profiling revealed Hex-3(Z)-enyl butyrate as a significant volatile compound in resistant accessions IIHR 4550 and IIHR-B-HP-79, in high concentrations suggesting that its production is not strictly species-specific effects as a synthetic volatile. Validation of Hex-3(Z)-enyl butyrate through bioassays and olfactometer studies demonstrated reduced scraping damage percentage at 8 μl-L and 16 μl-L concentrations in leaf dip bioassays. Four-arm olfactometer studies indicated that Hex-3(Z)-enyl butyrate significantly affected T.parvispinus time spent and entries at 16 μl-L. identified metabolites defences can serve as markers for breeding and also can be explored in pest management strategies.
辣椒因蓟马（thrps parvispinus, Karny）侵染而造成大量产量损失，因此需要可持续的抗性育种策略。了解抗性的生化基础将有助于寻找候选代谢物进行间接选择。对两种抗性辣椒（IIHR- b - hp -79、IIHR 4550）和两种敏感辣椒（IIHR 3455、IIHR 4604）进行了LC-MS和GC-MS分析。LC-MS分析显示，在易感菌株IIHR 3455中肌醇含量较高（8.74μg/g & 0.33μg/g； VIP评分分别为对照和侵染条件下的2 &； 2.5），表明其作为应激诱导代谢物而非抗性标记物。次生代谢物对抗性的贡献是基因型特异性的，可能是由这些代谢物之间复杂的相互作用驱动的。非目标叶片挥发性分析表明，Hex-3(Z)-烯基丁酸酯是抗性品种IIHR 4550和IIHR- b - hp -79中重要的挥发性化合物，其浓度较高，表明其作为一种合成挥发性物质的产生并不具有严格的种特异性。通过生物测定和嗅觉测定验证了hexx -3(Z)-丁酸烯酯在8 μl-L和16 μl-L浓度的叶浸生物测定中降低了刮伤率。四臂嗅觉测定结果表明，16 μl-L的hexx -3(Z)-烯酸酯显著影响了小叶蝉的停留时间和吸虫量。鉴定的代谢物防御可以作为育种标记，也可以在害虫管理策略中进行探索。
{"title":"Hex-3(Z)-Enyl Butyrate: A key volatile compound conferring resistance against South East Asian Thrips ( Thrips parvispinus ) in Capsicum spp","authors":"N Pavani, K S Shivashankara, N R Prasannakumar, D C Lakshmana Reddy, P D Kamala Jayanthi, R P Vasanthi, M Reddi Sekhar, Naresh Ponnam, K Madhavi Reddy","doi":"10.1093/hr/uhaf346","DOIUrl":"https://doi.org/10.1093/hr/uhaf346","url":null,"abstract":"Chilli incurs substantial yield losses due to Thrips parvispinus (Karny) infestation, necessitating sustainable resistance breeding strategies. Understanding biochemical basis of resistance will help in exploring the candidate metabolites for indirect selection. LC-MS and GC-MS profiling of two resistant (IIHR-B-HP-79, IIHR 4550) and two susceptible (IIHR 3455, IIHR 4604) chilli accessions were performed. LC-MS profiling revealed Inositol with higher levels in susceptible accession IIHR 3455 (8.74μg/g & 0.33μg/g; VIP score: 2 & 2.5 under control and infested conditions respectively), indicating its role as a stress-induced metabolite rather than a marker for resistance. Secondary metabolites contribution to resistance was genotype-specific and may possibly be driven by complex interactions among these metabolites. Untargeted leaf volatile profiling revealed Hex-3(Z)-enyl butyrate as a significant volatile compound in resistant accessions IIHR 4550 and IIHR-B-HP-79, in high concentrations suggesting that its production is not strictly species-specific effects as a synthetic volatile. Validation of Hex-3(Z)-enyl butyrate through bioassays and olfactometer studies demonstrated reduced scraping damage percentage at 8 μl-L and 16 μl-L concentrations in leaf dip bioassays. Four-arm olfactometer studies indicated that Hex-3(Z)-enyl butyrate significantly affected T.parvispinus time spent and entries at 16 μl-L. identified metabolites defences can serve as markers for breeding and also can be explored in pest management strategies.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"181 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145962095","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}
Banana, a globally important staple fruit, is naturally deficient in anthocyanins; however, successful engineering of anthocyanin-enriched banana has not been reported to date. Herein, a regulatory-network of five R2R3-MYBs (MusaUP1, MusaUP2, MbaMA2, MusaMA4, and MusaMA8) differentially synchronizing anthocyanin-biosynthesis in banana bract is reported. RNA-seq data of red-bract revealed a web of regulatory and structural-genes fine-tuning anthocyanin accumulation through amalgamation of MYBs and bHLHs activities. Y1H demonstrated differential affinities of these MusaMYBs to banana TT8, CHS, ANR, UFGT, FLS, ANS, and LAR, revealing an intricate pattern of layered-regulation in bract-pigmentation. Functional competence of this MYBs network resulted in intense anthocyanin-accumulation in whitish-onion and restoration of pigmentation in myb90/tt8 Arabidopsis seedlings. Hierarchical regulation in this MYB network stemmed in contrasting control over early and late flavonoid structural-genes as revealed by disparate orange-fluorescence of myb90/tt8 Arabidopsis-seedlings after DPBA-staining. In banana, a distinctive requirement of TT8 for pigmentation was observed for MbaMA2 and MusaMA8, while MusaUP1, MusaUP2, MusaMA4, were self-competent, although co-expression of MusaTT8 augmented the ectopic pigmentation-effect. Transcript abundance of flavonoid structural-genes in transgenic banana is in coherence with Y1H-data, thus catalysing pigmentation upto 500-fold over control. This regulatory MYBs hierarchical framework manifested flux in a spectrum of distinct pigment-metabolites, viz peonidin-3,5-diglucoside in MusaUP1 and MusaUP2, dalbergiodin in MbaMA2/TT8 lines (FLS-mediated pathway), leucodelphinidin and leucopelargonidin in MusaMA4 lines (DFR to ANS flux), and prodelphinidin B4 in MusaMA8 lines. This study will be a step forward towards metabolic-engineering for bio-fortification of banana and development of functional foods, as evident by strong antioxidant activities of these MYB lines.
{"title":"A coordinated network of MYB regulators orchestrates anthocyanin biosynthesis in Banana","authors":"Nandita Thakur, Rajni Kanwar, Akhil Singh Karchuli, Sanjana Negi","doi":"10.1093/hr/uhaf361","DOIUrl":"https://doi.org/10.1093/hr/uhaf361","url":null,"abstract":"Banana, a globally important staple fruit, is naturally deficient in anthocyanins; however, successful engineering of anthocyanin-enriched banana has not been reported to date. Herein, a regulatory-network of five R2R3-MYBs (MusaUP1, MusaUP2, MbaMA2, MusaMA4, and MusaMA8) differentially synchronizing anthocyanin-biosynthesis in banana bract is reported. RNA-seq data of red-bract revealed a web of regulatory and structural-genes fine-tuning anthocyanin accumulation through amalgamation of MYBs and bHLHs activities. Y1H demonstrated differential affinities of these MusaMYBs to banana TT8, CHS, ANR, UFGT, FLS, ANS, and LAR, revealing an intricate pattern of layered-regulation in bract-pigmentation. Functional competence of this MYBs network resulted in intense anthocyanin-accumulation in whitish-onion and restoration of pigmentation in myb90/tt8 Arabidopsis seedlings. Hierarchical regulation in this MYB network stemmed in contrasting control over early and late flavonoid structural-genes as revealed by disparate orange-fluorescence of myb90/tt8 Arabidopsis-seedlings after DPBA-staining. In banana, a distinctive requirement of TT8 for pigmentation was observed for MbaMA2 and MusaMA8, while MusaUP1, MusaUP2, MusaMA4, were self-competent, although co-expression of MusaTT8 augmented the ectopic pigmentation-effect. Transcript abundance of flavonoid structural-genes in transgenic banana is in coherence with Y1H-data, thus catalysing pigmentation upto 500-fold over control. This regulatory MYBs hierarchical framework manifested flux in a spectrum of distinct pigment-metabolites, viz peonidin-3,5-diglucoside in MusaUP1 and MusaUP2, dalbergiodin in MbaMA2/TT8 lines (FLS-mediated pathway), leucodelphinidin and leucopelargonidin in MusaMA4 lines (DFR to ANS flux), and prodelphinidin B4 in MusaMA8 lines. This study will be a step forward towards metabolic-engineering for bio-fortification of banana and development of functional foods, as evident by strong antioxidant activities of these MYB lines.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"30 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145962099","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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