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}
Venkateswara Rao Kadium, Ramesh Pilli, Andrej Svyantek, Zhuoyu Wang, John Stenger, Rajasekharreddy Bhoomireddy, Collin Auwarter, Xuehui Li, Harlene Hatterman-Valenti
Understanding the genetic control of fruit composition traits in interspecific grapevines (Vitis spp.) is crucial when breeding new cultivars with desirable fruit chemistry. To address this, a genome-wide association study (GWAS) was conducted using 587 genotypes derived from three elite selections. This study spanned three years (2020-to-2022) and with phenotyping conducted at three different timepoints within each season for a total of nine phenotyping events focused on nine fruit traits. Several strong and stable QTL associations were identified on chromosomes 6, 16, and 17 across multiple phenotyping events for most sugar and acid-related traits. Notably, putative sugar transporter genes Vitvi16g00860 and Vitvi16g00861 on chromosome 16, which facilitate the movement of sugars and K+ ions across membranes, were found to be associated with all sugar and acid traits studied. Additionally, several QTL on chromosomes 1-5, 7, 14, and 18 were identified for various fruit quality traits across different phenotyping events. We determined functional connections between traits and scrutinized candidate genes by utilizing gene ontology annotations for genes located near significant SNPs. We also highlighted the effect of different forms of phenotype (BLUPs and unmodified) in suppressing certain QTL associations. This GWAS study focused on fruit quality in grapes, establishing a necessary knowledge base regarding the genetic architecture of these traits to aid molecular breeders in further improving them.
{"title":"Dissecting the Genetic Basis of Relevant Fruit Quality Traits in Interspecific Grapevines ( Vitis spp.)","authors":"Venkateswara Rao Kadium, Ramesh Pilli, Andrej Svyantek, Zhuoyu Wang, John Stenger, Rajasekharreddy Bhoomireddy, Collin Auwarter, Xuehui Li, Harlene Hatterman-Valenti","doi":"10.1093/hr/uhaf353","DOIUrl":"https://doi.org/10.1093/hr/uhaf353","url":null,"abstract":"Understanding the genetic control of fruit composition traits in interspecific grapevines (Vitis spp.) is crucial when breeding new cultivars with desirable fruit chemistry. To address this, a genome-wide association study (GWAS) was conducted using 587 genotypes derived from three elite selections. This study spanned three years (2020-to-2022) and with phenotyping conducted at three different timepoints within each season for a total of nine phenotyping events focused on nine fruit traits. Several strong and stable QTL associations were identified on chromosomes 6, 16, and 17 across multiple phenotyping events for most sugar and acid-related traits. Notably, putative sugar transporter genes Vitvi16g00860 and Vitvi16g00861 on chromosome 16, which facilitate the movement of sugars and K+ ions across membranes, were found to be associated with all sugar and acid traits studied. Additionally, several QTL on chromosomes 1-5, 7, 14, and 18 were identified for various fruit quality traits across different phenotyping events. We determined functional connections between traits and scrutinized candidate genes by utilizing gene ontology annotations for genes located near significant SNPs. We also highlighted the effect of different forms of phenotype (BLUPs and unmodified) in suppressing certain QTL associations. This GWAS study focused on fruit quality in grapes, establishing a necessary knowledge base regarding the genetic architecture of these traits to aid molecular breeders in further improving them.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"6 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145903611","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}
Abdulqader Jighly, Norman Munyengwa, Reem Joukhadar, Vanika Garg, Natalie Dillon, Rhys G R Copeland, Jugpreet Singh, Sukhwinder Singh, Christopher I Cazzonelli, Penghao Wang, Peter Prentis, Craig Hardner, Rajeev K Varshney
Genomic prediction (GP) in mango breeding faces challenges due to the species’ complex biology, long cycles, and limited reference populations. To accelerate genetic improvement, this study integrated data from diverse global populations to increase the reference population size. It included three mango collections reserved in Australia (225), USA (161), and China (224), totalling 610 individuals. Fruit weight (FW) and total soluble solids (TSS) were measured in multiple datasets, while several other traits were measured in specific datasets. We evaluated genetic diversity, performed genome-wide association studies (GWAS), and assessed GP accuracy using standard, genotype-by-environment (GxE), and multi-trait models, both within and across collections. Findings revealed a highly admixed genetic structure, with faster linkage disequilibrium (LD) decay in the Chinese collection, indicating higher genetic diversity. Data integration significantly enhanced GWAS power, identifying 19 quantitative trait loci (QTL) for FW and 9 for TSS. GxE models consistently achieved higher or comparable prediction accuracies for FW and TSS compared to the non-GxE models, especially when combining Australian and USA collections. This was not the case when predicting into or from the Chinese collection, mostly due to differences in the phenotyping protocol. While single-trait models performed comparably to multi-trait models in predicting new individuals (Coss-Validation: CV1), multi-trait models significantly improved prediction accuracy in scenarios with incomplete phenotypic records (CV2). This study demonstrates that strategic global data integration significantly enhances GWAS power and GP accuracy in mango. This collaborative approach is crucial for developing more efficient and accelerated breeding programs for mango and other perennial trees.
{"title":"Strategic global data integration to improve genomic prediction accuracy in trees breeding programs facing resource limitations, a case study in mango","authors":"Abdulqader Jighly, Norman Munyengwa, Reem Joukhadar, Vanika Garg, Natalie Dillon, Rhys G R Copeland, Jugpreet Singh, Sukhwinder Singh, Christopher I Cazzonelli, Penghao Wang, Peter Prentis, Craig Hardner, Rajeev K Varshney","doi":"10.1093/hr/uhag004","DOIUrl":"https://doi.org/10.1093/hr/uhag004","url":null,"abstract":"Genomic prediction (GP) in mango breeding faces challenges due to the species’ complex biology, long cycles, and limited reference populations. To accelerate genetic improvement, this study integrated data from diverse global populations to increase the reference population size. It included three mango collections reserved in Australia (225), USA (161), and China (224), totalling 610 individuals. Fruit weight (FW) and total soluble solids (TSS) were measured in multiple datasets, while several other traits were measured in specific datasets. We evaluated genetic diversity, performed genome-wide association studies (GWAS), and assessed GP accuracy using standard, genotype-by-environment (GxE), and multi-trait models, both within and across collections. Findings revealed a highly admixed genetic structure, with faster linkage disequilibrium (LD) decay in the Chinese collection, indicating higher genetic diversity. Data integration significantly enhanced GWAS power, identifying 19 quantitative trait loci (QTL) for FW and 9 for TSS. GxE models consistently achieved higher or comparable prediction accuracies for FW and TSS compared to the non-GxE models, especially when combining Australian and USA collections. This was not the case when predicting into or from the Chinese collection, mostly due to differences in the phenotyping protocol. While single-trait models performed comparably to multi-trait models in predicting new individuals (Coss-Validation: CV1), multi-trait models significantly improved prediction accuracy in scenarios with incomplete phenotypic records (CV2). This study demonstrates that strategic global data integration significantly enhances GWAS power and GP accuracy in mango. This collaborative approach is crucial for developing more efficient and accelerated breeding programs for mango and other perennial trees.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"391 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145903626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alicja Macko-Podgórni, Kinga Zygmuntowicz, Wojciech Wesołowski, Kornelia Kwolek, Marcelina Skrabucha, Emilia Data, Zuzanna Boczar, Zara Maria Lacera, Charles Nathan Hancock, Dariusz Grzebelus
Transposable elements constitute a large portion of plant genomes and, due to their ability to change their genomic localization, they largely contribute to genome evolution and adaptability. Miniature inverted-repeat transposable elements (MITEs), due to their small size and localization near genes, seem to be a major source of potential functional variability. Effects imposed byMITEson the expression of associated genesthrough redistributing cis-regulatory elements have been postulated, but our knowledge in this area still remains limited. We showed that MITEs in the carrot genome are enriched with binding sites for LHY/RVE transcription factors. Experimental validation using DcLHY-DAP-seq not only confirmed the enrichment of DcLHY binding sites within MITEs but also demonstrated that elements from the DcTourist_15 family likely play a key role in redistributing these transcription factor binding sites. We showed that insertional polymorphisms of DcTourist_15 correspond with changes in the expression of associated genes, both in control conditions and in response to heat stress. In addition to placing individual genes under the control of DcLHY/RVE transcription factors, DcTourist_15 copies were found in promoters of genes involved in sulfur metabolism and cysteine biosynthesis. The enrichment of rice MITEs in OsLHY binding sites suggests the phenomenon of MITE-driven rewiring of LHY/RVE regulation may be more widespread across the plant kingdom. Carrot MITEs, particularly those from the DcTourist_15 family, drive evolution of the carrot genome, especially in the context of stress responsiveness, as they possibly fine-tune gene expression by redistributing binding sites for transcription factors from the LHY/RVE family.
{"title":"Cis-regulatory effects of carrot miniature inverted-repeat transposable elements on the expression of genes controlled by LHY/RVE transcription factors","authors":"Alicja Macko-Podgórni, Kinga Zygmuntowicz, Wojciech Wesołowski, Kornelia Kwolek, Marcelina Skrabucha, Emilia Data, Zuzanna Boczar, Zara Maria Lacera, Charles Nathan Hancock, Dariusz Grzebelus","doi":"10.1093/hr/uhaf360","DOIUrl":"https://doi.org/10.1093/hr/uhaf360","url":null,"abstract":"Transposable elements constitute a large portion of plant genomes and, due to their ability to change their genomic localization, they largely contribute to genome evolution and adaptability. Miniature inverted-repeat transposable elements (MITEs), due to their small size and localization near genes, seem to be a major source of potential functional variability. Effects imposed byMITEson the expression of associated genesthrough redistributing cis-regulatory elements have been postulated, but our knowledge in this area still remains limited. We showed that MITEs in the carrot genome are enriched with binding sites for LHY/RVE transcription factors. Experimental validation using DcLHY-DAP-seq not only confirmed the enrichment of DcLHY binding sites within MITEs but also demonstrated that elements from the DcTourist_15 family likely play a key role in redistributing these transcription factor binding sites. We showed that insertional polymorphisms of DcTourist_15 correspond with changes in the expression of associated genes, both in control conditions and in response to heat stress. In addition to placing individual genes under the control of DcLHY/RVE transcription factors, DcTourist_15 copies were found in promoters of genes involved in sulfur metabolism and cysteine biosynthesis. The enrichment of rice MITEs in OsLHY binding sites suggests the phenomenon of MITE-driven rewiring of LHY/RVE regulation may be more widespread across the plant kingdom. Carrot MITEs, particularly those from the DcTourist_15 family, drive evolution of the carrot genome, especially in the context of stress responsiveness, as they possibly fine-tune gene expression by redistributing binding sites for transcription factors from the LHY/RVE family.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"121 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145894329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Edda Francomano, Meriem Miyassa Aci, Saveria Mosca, Nesma Zakaria Mohamed, Giovanni Enrico Agosteo, Maria Giulia Li Destri Nicosia, Antonino Malacrinò, Leonardo Schena
Agriculture faces unprecedented challenges due to climate change, increasing food demand, and resource scarcity, which needs sustainable and innovative solutions. This review explores the emerging paradigm of holobiont biology (host and its microbiome as biological unit) in the context of emerging plant health challenges driven by global changes. We highlight three critical challenges: the rise of complex plant syndromes, the emergence and re-emergence of plant diseases, and the consequences of dysbiotic plant microbiomes. We discuss how microbiome-based strategies can enhance plant resilience, reduce reliance on agrochemicals, and foster sustainable agriculture. Integrating these strategies with advanced frameworks, such as holo-omics and machine learning, opens avenues for microbiome-based solutions to address agricultural challenges in the era of global changes, ensuring resilient crop systems and planetary health.
{"title":"Plant health in the era of global changes, holobiont biology, and microbiome-based solutions","authors":"Edda Francomano, Meriem Miyassa Aci, Saveria Mosca, Nesma Zakaria Mohamed, Giovanni Enrico Agosteo, Maria Giulia Li Destri Nicosia, Antonino Malacrinò, Leonardo Schena","doi":"10.1093/hr/uhaf364","DOIUrl":"https://doi.org/10.1093/hr/uhaf364","url":null,"abstract":"Agriculture faces unprecedented challenges due to climate change, increasing food demand, and resource scarcity, which needs sustainable and innovative solutions. This review explores the emerging paradigm of holobiont biology (host and its microbiome as biological unit) in the context of emerging plant health challenges driven by global changes. We highlight three critical challenges: the rise of complex plant syndromes, the emergence and re-emergence of plant diseases, and the consequences of dysbiotic plant microbiomes. We discuss how microbiome-based strategies can enhance plant resilience, reduce reliance on agrochemicals, and foster sustainable agriculture. Integrating these strategies with advanced frameworks, such as holo-omics and machine learning, opens avenues for microbiome-based solutions to address agricultural challenges in the era of global changes, ensuring resilient crop systems and planetary health.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"53 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145894330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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