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}
Trifolium pratense L. is a multifunctional crop of agronomic importance for forage, horticulture, and ecological restoration. However, the lack of a high-quality genome assembly and the limited representation of genetic diversity by a single reference have impeded its genetic research and molecular breeding. Here, we present the first telomere-to-telomere (T2T) gap-free genome for the diploid (2n = 2x = 14) cultivar T. pratense cv. ‘Zhongtian No. 5’ (TpraZt5), assembled through an integrated sequencing strategy. The 390.94 Mb assembly demonstrates high quality, with a base accuracy > 98.5%, 98.1% BUSCO completeness, a long terminal repeat assembly index of 25.65, and a contig N50 of 52.95 Mb. We annotated 35 971 protein-coding genes and found repeat sequences accounting for 59.6% of the genome. The assembly resolved all seven centromeres and 14 telomeres, providing unprecedented insight into these complex genomic regions. We further constructed a 480.76 Mb pan-genome by integrating two additional accessions, which classified genes into core (70.2%), dispensable (25.3%), and private (4.5%) sets. Comparative genomic analyses identified 606 species-specific genes in TpraZt5 and uncovered extensive structural variations. Functional investigations revealed four species-specific genes and six contracted genes associated with isoflavonoid biosynthesis, two expanded chlorophyll a-b binding proteins, and seven expanded auxin-related genes that may contribute to the high productivity of TpraZt5. Additionally, 44 Gypsy-type transposons within the zeatin biosynthesis pathway were identified as potential regulators of trifoliate leaf development. These genomic resources substantially improve structural annotation and functional characterization, providing vital tools for gene discovery and enhancing molecular breeding initiatives in red clover.
{"title":"A telomere-to-telomere gap-free genome of the new cultivar ‘Zhongtian No. 5,’ combined with pan-genome analysis, aids in exploration and genetic enhancement of red clover ( Trifolium pratense L.)","authors":"Guangxin Cui, Chunmei Wang, Tianfen Guo, Fang Wu, Xia Wen, Xuehui Zhou, Biao Song, Jing Zhang, Xinqiang Zhu, Qian Zhang, Yuan Lu, Huirong Duan, Hongshan Yang","doi":"10.1093/hr/uhag013","DOIUrl":"https://doi.org/10.1093/hr/uhag013","url":null,"abstract":"Trifolium pratense L. is a multifunctional crop of agronomic importance for forage, horticulture, and ecological restoration. However, the lack of a high-quality genome assembly and the limited representation of genetic diversity by a single reference have impeded its genetic research and molecular breeding. Here, we present the first telomere-to-telomere (T2T) gap-free genome for the diploid (2n = 2x = 14) cultivar T. pratense cv. ‘Zhongtian No. 5’ (TpraZt5), assembled through an integrated sequencing strategy. The 390.94 Mb assembly demonstrates high quality, with a base accuracy > 98.5%, 98.1% BUSCO completeness, a long terminal repeat assembly index of 25.65, and a contig N50 of 52.95 Mb. We annotated 35 971 protein-coding genes and found repeat sequences accounting for 59.6% of the genome. The assembly resolved all seven centromeres and 14 telomeres, providing unprecedented insight into these complex genomic regions. We further constructed a 480.76 Mb pan-genome by integrating two additional accessions, which classified genes into core (70.2%), dispensable (25.3%), and private (4.5%) sets. Comparative genomic analyses identified 606 species-specific genes in TpraZt5 and uncovered extensive structural variations. Functional investigations revealed four species-specific genes and six contracted genes associated with isoflavonoid biosynthesis, two expanded chlorophyll a-b binding proteins, and seven expanded auxin-related genes that may contribute to the high productivity of TpraZt5. Additionally, 44 Gypsy-type transposons within the zeatin biosynthesis pathway were identified as potential regulators of trifoliate leaf development. These genomic resources substantially improve structural annotation and functional characterization, providing vital tools for gene discovery and enhancing molecular breeding initiatives in red clover.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"49 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145962100","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}
Qin Chen, Xiaoying Wu, Yuan Qu, Na Li, Xiuming Cui, Feng Ge
Sucrose synthase (SUS) is a pivotal enzyme bridging primary carbon metabolism and secondary biosynthesis in plants. In Panax notoginseng, we demonstrate that sucrose synthase 1 (PnSUS1) serves as a metabolic bottleneck for saponin glycosylation by supplying UDP-glucose. PnWRKY38 was identified as a WRKY transcription factor whose expression correlated with both PnSUS1 and saponin accumulation. Overexpression of PnWRKY38 could up-regulate PnSUS1 expression by 3.5-fold, increase SUS enzyme activity by 2.8-fold and elevate UDP-glucose pools by 68%. Consequently, the total content of ginsenosides Rg1, Rb1 and Rd rose by 2.1–2.4-fold. Conversely, PnSUS1 or PnWRKY38 suppression reduced UDP-glucose available and saponin biosynthesis by > 50%. Y1H and luciferase assays indicated that PnWRKY38 directly activated PnSUS1 expression by binding to W-box motifs in its promoter. These results not only illustrate the specific function that PnSUS1 executes in UDPG biosynthesis but also reveal a new WRKY transcriptional regulatory module regulating notoginsenosides production.
{"title":"PnWRKY38-PnSUS1 axis regulates the biosynthesis of Panax notoginseng saponins","authors":"Qin Chen, Xiaoying Wu, Yuan Qu, Na Li, Xiuming Cui, Feng Ge","doi":"10.1093/hr/uhag012","DOIUrl":"https://doi.org/10.1093/hr/uhag012","url":null,"abstract":"Sucrose synthase (SUS) is a pivotal enzyme bridging primary carbon metabolism and secondary biosynthesis in plants. In Panax notoginseng, we demonstrate that sucrose synthase 1 (PnSUS1) serves as a metabolic bottleneck for saponin glycosylation by supplying UDP-glucose. PnWRKY38 was identified as a WRKY transcription factor whose expression correlated with both PnSUS1 and saponin accumulation. Overexpression of PnWRKY38 could up-regulate PnSUS1 expression by 3.5-fold, increase SUS enzyme activity by 2.8-fold and elevate UDP-glucose pools by 68%. Consequently, the total content of ginsenosides Rg1, Rb1 and Rd rose by 2.1–2.4-fold. Conversely, PnSUS1 or PnWRKY38 suppression reduced UDP-glucose available and saponin biosynthesis by > 50%. Y1H and luciferase assays indicated that PnWRKY38 directly activated PnSUS1 expression by binding to W-box motifs in its promoter. These results not only illustrate the specific function that PnSUS1 executes in UDPG biosynthesis but also reveal a new WRKY transcriptional regulatory module regulating notoginsenosides production.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"265 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145961655","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}
Zhiwei Liu, Yan Ma, Teng Wang, Qiuyue Chen, Dihan Yang, Yiqing Guan, Tianyuan Yang, Ming Zhao
Glutamate synthase (GOGAT) is crucial for nitrogen metabolism and amino acid biosynthesis in tea plants, yet the post-transcriptional regulation of GOGAT remains unclear. This study identified miR1507c as a direct interactor of CsNADH-GOGAT, confirmed by DLR assays and 5’RLM-RACE. Notably in tobacco, the relative luciferase activity in plants overexpressing CsNADH-GOGAT and co-expressing miR1507c + CsNADH-GOGATm3 (mutant) were significantly higher than in those co-expressing miR1507c + CsNADH-GOGAT. Overexpression of miR1507c also significantly suppressed the expression of CsNADH-GOGAT and endogenous NtNADH-GOGAT homologs. Leveraging lncRNA sequencing, we screened lncR12304.1 as a ceRNA that regulates CsNADH-GOGAT by competitively binding to miR1507c. Cytoplasmic co-localization (validated by FISH) and direct interaction (confirmed by DLR assays) between lncR12304.1 and miR1507c were established. RNA pull down-qPCR further demonstrated miR1507c binding to both lncR12304.1 and CsNADH-GOGAT. The regulatory axis lncR12304.1–miR1507c–CsNADH-GOGAT was substantiated in vivo: (1) in tea roots/shoots under varying nitrogen treatments and following miR1507c suppression using Antagomir, and (2) in tobacco via transient co-overexpression. Collectively, our results demonstrate the establishment of this ceRNA network and its role in regulating glutamate and theanine biosynthesis.
{"title":"LncR12304.1-miR1507c- CsNADH-GOGAT ceRNA module regulates amino acid biosynthesis in tea plant ( Camellia sinensis )","authors":"Zhiwei Liu, Yan Ma, Teng Wang, Qiuyue Chen, Dihan Yang, Yiqing Guan, Tianyuan Yang, Ming Zhao","doi":"10.1093/hr/uhag014","DOIUrl":"https://doi.org/10.1093/hr/uhag014","url":null,"abstract":"Glutamate synthase (GOGAT) is crucial for nitrogen metabolism and amino acid biosynthesis in tea plants, yet the post-transcriptional regulation of GOGAT remains unclear. This study identified miR1507c as a direct interactor of CsNADH-GOGAT, confirmed by DLR assays and 5’RLM-RACE. Notably in tobacco, the relative luciferase activity in plants overexpressing CsNADH-GOGAT and co-expressing miR1507c + CsNADH-GOGATm3 (mutant) were significantly higher than in those co-expressing miR1507c + CsNADH-GOGAT. Overexpression of miR1507c also significantly suppressed the expression of CsNADH-GOGAT and endogenous NtNADH-GOGAT homologs. Leveraging lncRNA sequencing, we screened lncR12304.1 as a ceRNA that regulates CsNADH-GOGAT by competitively binding to miR1507c. Cytoplasmic co-localization (validated by FISH) and direct interaction (confirmed by DLR assays) between lncR12304.1 and miR1507c were established. RNA pull down-qPCR further demonstrated miR1507c binding to both lncR12304.1 and CsNADH-GOGAT. The regulatory axis lncR12304.1–miR1507c–CsNADH-GOGAT was substantiated in vivo: (1) in tea roots/shoots under varying nitrogen treatments and following miR1507c suppression using Antagomir, and (2) in tobacco via transient co-overexpression. Collectively, our results demonstrate the establishment of this ceRNA network and its role in regulating glutamate and theanine biosynthesis.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"391 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145962101","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}
Carmen Martín-Pizarro, María Florencia Perotti, José M Franco-Zorrilla, Rosa Lozano-Durán, Guozheng Qin, David Posé
Ripening Inducing Factor (RIF) is a key NAC transcription factor regulating strawberry fruit ripening. Previous studies using RIF-RNAi and overexpression lines in Fragaria × ananassa and CRISPR knock-out lines in F. vesca have established the role of RIF in controlling ABA biosynthesis and signaling, cell wall remodeling, and secondary metabolism. In this study, we deciphered FaRIF’s transcriptional regulatory network by combining ChIP-seq-based identification of its direct targets with an analysis of FaRIF-RNAi transcriptome data. These analyses revealed FaRIF’s direct role in multiple aspects of strawberry fruit ripening, including the regulation of ripening-related transcription factors, phytohormone content and signaling, primary and secondary metabolism, and cell wall degradation. Additionally, using the TurboID-based proximity labeling approach, we have identified FaRIF interactors, including proteins involved in mRNA and protein homeostasis, as well as several NAC transcription factors. Among these, FaNAC021 and FaNAC034 were found to potentially cooperate with FaRIF to enhance the transcription of shared target genes. This integrative analysis, combining transcriptome analysis, in vivo ChIP-seq, and proximity labeling, broadens our understanding of FaRIF-mediated transcriptional networks and interaction partners, providing valuable insights into the molecular regulation of strawberry fruit ripening by this transcription factor.
RIF是调控草莓果实成熟的关键NAC转录因子。先前利用RIF- rnai和Fragaria x ananassa过表达系和F. vesca CRISPR敲除系的研究已经确定了RIF在控制ABA生物合成和信号转导、细胞壁重塑和次生代谢中的作用。在这项研究中，我们通过结合基于chip -seq的直接靶标鉴定和FaRIF- rnai转录组数据分析，破译了FaRIF的转录调控网络。这些分析揭示了FaRIF在草莓果实成熟的多个方面的直接作用，包括调控成熟相关转录因子、植物激素含量和信号、初级和次级代谢以及细胞壁降解。此外，使用基于turboid的接近标记方法，我们已经确定了FaRIF相互作用物，包括mRNA和蛋白质稳态相关的蛋白质，以及几个NAC转录因子。其中，FaNAC021和FaNAC034被发现可能与FaRIF合作，增强共享靶基因的转录。这种综合分析，结合转录组分析，体内ChIP-seq和邻近标记，拓宽了我们对farif介导的转录网络和相互作用伙伴的理解，为该转录因子对草莓果实成熟的分子调控提供了有价值的见解。
{"title":"FaRIF as a Key Regulator of Strawberry Fruit Ripening: Deciphering its Targets and Interaction Networks","authors":"Carmen Martín-Pizarro, María Florencia Perotti, José M Franco-Zorrilla, Rosa Lozano-Durán, Guozheng Qin, David Posé","doi":"10.1093/hr/uhaf362","DOIUrl":"https://doi.org/10.1093/hr/uhaf362","url":null,"abstract":"Ripening Inducing Factor (RIF) is a key NAC transcription factor regulating strawberry fruit ripening. Previous studies using RIF-RNAi and overexpression lines in Fragaria × ananassa and CRISPR knock-out lines in F. vesca have established the role of RIF in controlling ABA biosynthesis and signaling, cell wall remodeling, and secondary metabolism. In this study, we deciphered FaRIF’s transcriptional regulatory network by combining ChIP-seq-based identification of its direct targets with an analysis of FaRIF-RNAi transcriptome data. These analyses revealed FaRIF’s direct role in multiple aspects of strawberry fruit ripening, including the regulation of ripening-related transcription factors, phytohormone content and signaling, primary and secondary metabolism, and cell wall degradation. Additionally, using the TurboID-based proximity labeling approach, we have identified FaRIF interactors, including proteins involved in mRNA and protein homeostasis, as well as several NAC transcription factors. Among these, FaNAC021 and FaNAC034 were found to potentially cooperate with FaRIF to enhance the transcription of shared target genes. This integrative analysis, combining transcriptome analysis, in vivo ChIP-seq, and proximity labeling, broadens our understanding of FaRIF-mediated transcriptional networks and interaction partners, providing valuable insights into the molecular regulation of strawberry fruit ripening by this transcription factor.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"29 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145903610","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}
Kiwifruit plants are much damaged by several days of waterlogging stress. The effect can be a serious problem for the growers in the lowlands or plain areas where floods cannot be drained timely. Actinidia valvata is a polyploid species that has been widely used as waterlogging resistant rootstock in kiwifruit cultivation. Here we report haplotype-resolved chromosome-scale assemblies of an Actinidia valvata male plant ‘DE,’ defining two subgenomes, a diploid closely related to A. polygama and an autotetraploid closely related to A. macrosperma as their ancestral contributors, respectively, together to form an allohexaploid. Genome-wide comparisons of the assembled 174 pseudochromosomes with nine distinct Actinidia species revealed the genomic structure, phylogeny and duplication history of ‘DE’ genome. Evolutionary analyses suggest that it was formed approximately 0.44 to 0.88 Mya and evolved by a recent alloploid addition to an autotetraploid ancestor. Annotation of sex determining genes (SyGl and FrBy) on Y chromosome unraveled that the chromosomal location and organization of sex determining region (SDR) are conserved to and share an identical lineage with A. polygama, the diploid ancestor. Comprehensive transcriptome analysis indicates that its enhanced waterlogging tolerance is due to the restricted activation of anaerobic survival genes and the consequence with prolonged carbohydrate supply to keep the root system quiescently alive under hypoxia. Our study provides valuable genomic resources and offers insights into the evolution and the underlying mechanism of enhanced waterlogging tolerance of A. valvata hexaploid.
{"title":"Haplotype-resolved genome assembly provides insights into the evolutionary origin of waterlogging-tolerant Actinidia valvata hexaploid","authors":"Feng Zhang, Yunzhi Lin, Yingzhen Wang, Binglong Li, Hongtao Wang, Ying Wu, Yanyan Zhu, Xiuhong Zhou, Wangmei Ren, Lihuan Wang, Ying Yang, Songhu Wang, Junyang Yue, Pengpeng Zheng, Yongsheng Liu","doi":"10.1093/hr/uhag011","DOIUrl":"https://doi.org/10.1093/hr/uhag011","url":null,"abstract":"Kiwifruit plants are much damaged by several days of waterlogging stress. The effect can be a serious problem for the growers in the lowlands or plain areas where floods cannot be drained timely. Actinidia valvata is a polyploid species that has been widely used as waterlogging resistant rootstock in kiwifruit cultivation. Here we report haplotype-resolved chromosome-scale assemblies of an Actinidia valvata male plant ‘DE,’ defining two subgenomes, a diploid closely related to A. polygama and an autotetraploid closely related to A. macrosperma as their ancestral contributors, respectively, together to form an allohexaploid. Genome-wide comparisons of the assembled 174 pseudochromosomes with nine distinct Actinidia species revealed the genomic structure, phylogeny and duplication history of ‘DE’ genome. Evolutionary analyses suggest that it was formed approximately 0.44 to 0.88 Mya and evolved by a recent alloploid addition to an autotetraploid ancestor. Annotation of sex determining genes (SyGl and FrBy) on Y chromosome unraveled that the chromosomal location and organization of sex determining region (SDR) are conserved to and share an identical lineage with A. polygama, the diploid ancestor. Comprehensive transcriptome analysis indicates that its enhanced waterlogging tolerance is due to the restricted activation of anaerobic survival genes and the consequence with prolonged carbohydrate supply to keep the root system quiescently alive under hypoxia. Our study provides valuable genomic resources and offers insights into the evolution and the underlying mechanism of enhanced waterlogging tolerance of A. valvata hexaploid.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"28 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145937998","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}
Zhuoyi Liu, Yimeng Wang, Hang Zhang, Zidi He, Zhiqi Li, Ke Ma, Minglei Zhao, Jianguo Li, Xingshuai Ma
Fatty acid-derived volatile organic compounds (VOC), especially C6 and C9 aldehydes and alcohols, are vital contributors to the fresh aroma of fruits. However, the specific volatiles responsible for this freshness and their biosynthetic regulatory mechanisms remain poorly characterized in litchi (Litchi chinensis Sonn.). In this study, we systematically characterized the VOC profiles of 24 representative litchi cultivars and identified four critical compounds—trans,cis-2,6-nonadien-1-ol, 1-hexanol, (E)-6-nonenal, and (E)-2-hexen-1-ol—as primary determinants of fresh-aroma variation. Weighted gene co-expression network analysis of the transcriptomic data, corroborated by RT-qPCR, revealed a strong positive correlation between the expression of LcLOX7 and the abundance of these key fresh-aroma volatiles. Functional characterization via LcLOX7 overexpression in litchi callus and tomato fruits validated its pivotal role in enhancing the biosynthesis of fatty acid-derived VOCs, specifically C9 volatiles. Subsequent in vivo and in vitro assays confirmed the direct transcriptional activation of LcLOX7 by two transcription factors (TF), LcARF17 and LcRAP2–4. The expression patterns of these TFs correlated with the accumulation of key fresh-aroma volatiles across different litchi cultivars and paralleled LcLOX7 expression during fruit ripening. Moreover, overexpression and silencing of LcARF17 or LcRAP2–4 in litchi callus validated their regulatory function in promoting C9 volatile synthesis. Our findings collectively support a regulatory model wherein the LcARF17/LcRAP2–4–LcLOX7 module orchestrates the biosynthesis of fresh aroma in litchi fruit. Notably, this study provides the first evidence that ARF transcription factor participates in the formation of fresh fruit aroma, thereby offering novel insights for the molecular breeding of flavor quality in fruit crops.
{"title":"Involvement of the LcARF17- and LcRAP2–4-LcLOX7 regulatory modules in the biosynthesis of fresh aroma in litchi aril","authors":"Zhuoyi Liu, Yimeng Wang, Hang Zhang, Zidi He, Zhiqi Li, Ke Ma, Minglei Zhao, Jianguo Li, Xingshuai Ma","doi":"10.1093/hr/uhag010","DOIUrl":"https://doi.org/10.1093/hr/uhag010","url":null,"abstract":"Fatty acid-derived volatile organic compounds (VOC), especially C6 and C9 aldehydes and alcohols, are vital contributors to the fresh aroma of fruits. However, the specific volatiles responsible for this freshness and their biosynthetic regulatory mechanisms remain poorly characterized in litchi (Litchi chinensis Sonn.). In this study, we systematically characterized the VOC profiles of 24 representative litchi cultivars and identified four critical compounds—trans,cis-2,6-nonadien-1-ol, 1-hexanol, (E)-6-nonenal, and (E)-2-hexen-1-ol—as primary determinants of fresh-aroma variation. Weighted gene co-expression network analysis of the transcriptomic data, corroborated by RT-qPCR, revealed a strong positive correlation between the expression of LcLOX7 and the abundance of these key fresh-aroma volatiles. Functional characterization via LcLOX7 overexpression in litchi callus and tomato fruits validated its pivotal role in enhancing the biosynthesis of fatty acid-derived VOCs, specifically C9 volatiles. Subsequent in vivo and in vitro assays confirmed the direct transcriptional activation of LcLOX7 by two transcription factors (TF), LcARF17 and LcRAP2–4. The expression patterns of these TFs correlated with the accumulation of key fresh-aroma volatiles across different litchi cultivars and paralleled LcLOX7 expression during fruit ripening. Moreover, overexpression and silencing of LcARF17 or LcRAP2–4 in litchi callus validated their regulatory function in promoting C9 volatile synthesis. Our findings collectively support a regulatory model wherein the LcARF17/LcRAP2–4–LcLOX7 module orchestrates the biosynthesis of fresh aroma in litchi fruit. Notably, this study provides the first evidence that ARF transcription factor participates in the formation of fresh fruit aroma, thereby offering novel insights for the molecular breeding of flavor quality in fruit crops.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"28 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145937997","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 tender shoots of tea plant [Camellia sinensis (L.) Kuntze] contain characteristic flavor metabolites such as catechins, caffeine, and theanine, which are the raw materials for making various types of high-quality tea. The gene expression profiles with spatial information for tea shoots remain unclear, which has hindered the exploration of precise regulatory mechanisms of these characteristic metabolites in different cell types. Here, we provided a high-throughput analysis of the spatial gene expression of the tea shoot, including the apical bud, young leaf, and stem. The genome-wide expression pattern was delineated into nine representative spatial co-expression clusters, and cell type identification was achieved by integrating histological structures with marker gene annotation. The dynamic differentiation processes of cells in leaf and bud were revealed through the reconstruction of pseudotemporal trajectories, uncovering the coupling relationship between spatial organization and developmental progression. GO enrichment analysis indicated that different clusters were enriched in functional pathways such as photosynthesis, cell wall construction, substance transport, and hormone response during differentiation, demonstrating their stage-specific expression throughout development. Additionally, we found that structural genes associated with the metabolism of catechins, theanine, and caffeine exhibited distinct spatial expression patterns across various tissues. Based on functional verification, we identified that the transcription factor gene CsTCP4 could positively regulate the biosynthesis of catechins and the hydrolysis of theanine. In conclusion, the ST atlas provides a foundational dataset for understanding gene expression heterogeneity in tea shoots and expands our understanding of the synergistic regulation of theanine and catechin metabolism in tea.
{"title":"Spatial transcriptome analysis of the tea tender shoot sheds light on transcriptional regulation of characteristic metabolites","authors":"Cheng Zhang, Chengzhe Zhou, Caiyun Tian, Shengjing Wen, Zhendong Zhang, Anru Zheng, Zhenhan Rui, Yuting Li, Shuaibo Shao, Siwei Deng, Zhong Wang, Yuqiong Guo","doi":"10.1093/hr/uhag003","DOIUrl":"https://doi.org/10.1093/hr/uhag003","url":null,"abstract":"The tender shoots of tea plant [Camellia sinensis (L.) Kuntze] contain characteristic flavor metabolites such as catechins, caffeine, and theanine, which are the raw materials for making various types of high-quality tea. The gene expression profiles with spatial information for tea shoots remain unclear, which has hindered the exploration of precise regulatory mechanisms of these characteristic metabolites in different cell types. Here, we provided a high-throughput analysis of the spatial gene expression of the tea shoot, including the apical bud, young leaf, and stem. The genome-wide expression pattern was delineated into nine representative spatial co-expression clusters, and cell type identification was achieved by integrating histological structures with marker gene annotation. The dynamic differentiation processes of cells in leaf and bud were revealed through the reconstruction of pseudotemporal trajectories, uncovering the coupling relationship between spatial organization and developmental progression. GO enrichment analysis indicated that different clusters were enriched in functional pathways such as photosynthesis, cell wall construction, substance transport, and hormone response during differentiation, demonstrating their stage-specific expression throughout development. Additionally, we found that structural genes associated with the metabolism of catechins, theanine, and caffeine exhibited distinct spatial expression patterns across various tissues. Based on functional verification, we identified that the transcription factor gene CsTCP4 could positively regulate the biosynthesis of catechins and the hydrolysis of theanine. In conclusion, the ST atlas provides a foundational dataset for understanding gene expression heterogeneity in tea shoots and expands our understanding of the synergistic regulation of theanine and catechin metabolism in tea.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"82 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145920213","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}
Changsheng Zhai, Yating Li, Jie Li, Pingyin Guan, Juan Jin, Wensuo Jia
The control of fruit quality is of major scientific, nutritional, and commercial importance. In addition to being influenced by the intrinsic characteristics of each fruit species, fruit quality development is largely modulated by environmental factors. The environmental modulation of fruit quality primarily involves a signal transduction process that links environmental perception to the transcriptional or post-transcriptional regulation of key enzymes participating in fruit quality–associated metabolisms. Over the past decades, the effects of environmental factors on fruit quality traits have been extensively studied, and increasing attention has been directed toward elucidating the signaling mechanisms that govern this environmental modulation. However, knowledge in this research area has not yet been systematically summarized. In this review, we first provide an overview of the physiological and molecular bases underlying the modulation of fruit quality development by the three major environmental factors: water deficit, salinity, and temperature stresses. We then summarize recent advances in understanding the signaling mechanisms that mediate the environmental modulation of fruit quality development. Finally, we propose several perspectives to facilitate comprehension and guide future research endeavors.
{"title":"Signaling mechanisms governing the environmental modulation of fruit quality development","authors":"Changsheng Zhai, Yating Li, Jie Li, Pingyin Guan, Juan Jin, Wensuo Jia","doi":"10.1093/hr/uhag005","DOIUrl":"https://doi.org/10.1093/hr/uhag005","url":null,"abstract":"The control of fruit quality is of major scientific, nutritional, and commercial importance. In addition to being influenced by the intrinsic characteristics of each fruit species, fruit quality development is largely modulated by environmental factors. The environmental modulation of fruit quality primarily involves a signal transduction process that links environmental perception to the transcriptional or post-transcriptional regulation of key enzymes participating in fruit quality–associated metabolisms. Over the past decades, the effects of environmental factors on fruit quality traits have been extensively studied, and increasing attention has been directed toward elucidating the signaling mechanisms that govern this environmental modulation. However, knowledge in this research area has not yet been systematically summarized. In this review, we first provide an overview of the physiological and molecular bases underlying the modulation of fruit quality development by the three major environmental factors: water deficit, salinity, and temperature stresses. We then summarize recent advances in understanding the signaling mechanisms that mediate the environmental modulation of fruit quality development. Finally, we propose several perspectives to facilitate comprehension and guide future research endeavors.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"47 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145920212","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}
Hu Sun, Kaixing Pang, Xuemei Zhou, Luyao Wang, Binrong Li, Jiaxue Wei, Huiyan Guo, Yucheng Wang
Drought is a major abiotic stress that poses a significant threat to plants. Basic leucine zipper (bZIP) transcription factors (TFs) are important for plant stress signal transduction. However, the specific functions and molecular mechanisms of bZIP TFs under drought stress are still unclear. In this study, a BpbZIP4 TF of Betula platyphylla (birch) that responds strongly to drought stress was identified. Transgenic birch plants with BpbZIP4 overexpression and RNA interference were developed for gain- and loss-of-function assays. Results from phenotypic, staining, and physiological analyses showed that BpbZIP4 significantly enhances drought resistance and promotes root growth in birch. A four-layer drought-responsive gene regulatory network (GRN) was constructed based on BpbZIP4 transgenic lines. ChIP-PCR and qRT-PCR assays verified the putative interactions among genes at different hierarchical levels, confirming the reliability of the GRN. TF-Centered Y1H, ChIP, and GUS assays revealed that BpbZIP4 regulates the expression of second-layer TFs in the GRN by binding to two novel elements and one photosynthesis-responsive element. Furthermore, six randomly selected second-layer GRN TFs (BpMYB61, BpBEL1, BpWOX4, BpbHLH100, BpZAT11 and BpHB17), when transformed into birch plants, significantly influence birch’s drought tolerance. These results indicate that BpbZIP4 regulates second-layer TFs, thereby hierarchically relaying signals to bottom-layer functional genes, engaging multiple biological pathways, and ultimately enhancing drought resistance in birch. Collectively, these findings clarify the drought regulatory mechanism of BpbZIP4 and identify additional key genes for breeding drought-resistant birch varieties.
{"title":"A BpbZIP4 Transcription Factor Enhances Drought Resistance and Root Development in Betula platyphylla : Insights from a Gene Regulatory Network","authors":"Hu Sun, Kaixing Pang, Xuemei Zhou, Luyao Wang, Binrong Li, Jiaxue Wei, Huiyan Guo, Yucheng Wang","doi":"10.1093/hr/uhag002","DOIUrl":"https://doi.org/10.1093/hr/uhag002","url":null,"abstract":"Drought is a major abiotic stress that poses a significant threat to plants. Basic leucine zipper (bZIP) transcription factors (TFs) are important for plant stress signal transduction. However, the specific functions and molecular mechanisms of bZIP TFs under drought stress are still unclear. In this study, a BpbZIP4 TF of Betula platyphylla (birch) that responds strongly to drought stress was identified. Transgenic birch plants with BpbZIP4 overexpression and RNA interference were developed for gain- and loss-of-function assays. Results from phenotypic, staining, and physiological analyses showed that BpbZIP4 significantly enhances drought resistance and promotes root growth in birch. A four-layer drought-responsive gene regulatory network (GRN) was constructed based on BpbZIP4 transgenic lines. ChIP-PCR and qRT-PCR assays verified the putative interactions among genes at different hierarchical levels, confirming the reliability of the GRN. TF-Centered Y1H, ChIP, and GUS assays revealed that BpbZIP4 regulates the expression of second-layer TFs in the GRN by binding to two novel elements and one photosynthesis-responsive element. Furthermore, six randomly selected second-layer GRN TFs (BpMYB61, BpBEL1, BpWOX4, BpbHLH100, BpZAT11 and BpHB17), when transformed into birch plants, significantly influence birch’s drought tolerance. These results indicate that BpbZIP4 regulates second-layer TFs, thereby hierarchically relaying signals to bottom-layer functional genes, engaging multiple biological pathways, and ultimately enhancing drought resistance in birch. Collectively, these findings clarify the drought regulatory mechanism of BpbZIP4 and identify additional key genes for breeding drought-resistant birch varieties.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"51 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145903711","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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