Qianru Ma, Zhi Zhao, Kede Liu, Huaxin Li, Youjuan Quan, Long Wang, Hongping Zhao, Damei Pei, Guoyong Tang, Liang Xu, Lu Xiao, Dezhi Du
Spring-type Brassica rapa L. is a valuable genetic resource for breeding early-maturing crops, offering advantages such as early flowering and rapid maturation. However, the genetic mechanisms governing flowering time (FT) in spring-type B. rapa remain insufficiently understood. In this study, we investigated the flowering-time trait of an extremely early-maturing landrace, “Haoyou 11”, originating from the Qinghai-Tibetan Plateau. Initial mapping was conducted using an F2 population derived from the cross between Haoyou 11 and Dahuang (a late-flowering spring-type landrace of B. rapa). A major quantitative trait locus (QTL) for flowering time, designated qFTA06, was identified within a 1.70 Mb interval on chromosome A06 using genotyping-by-sequencing (GBS) and bulked segregant analysis sequencing (BSA-seq). The locus qFTA06 was subsequently fine-mapped to a 75.16 kb region with a set of near-isogenic lines (NILs), and BrCDF3, a gene encoding a Dof transcription factor, was identified as the causal gene underlying qFTA06. Virus-induced gene silencing (VIGS) experiments revealed that BrCDF3 acts as a negative regulator of flowering time under long-day (LD) conditions, with sequence variation contributing to the early-flowering phenotype in Haoyou 11. Phenotypic analysis of NILs showed that NIL-E, carrying the BrCDF3 allele from Haoyou 11, flowered approximately 7 days earlier than NIL-L, which harbors the BrCDF3 allele from Dahuang. By employing CRISPR/Cas9 technology, we further validated that the homologous gene BnCDF3 also functions as a negative regulator of flowering time in Brassica napus L., and analyzed natural variations in the CDF3 gene across natural populations. This study provides new insights into the genetic basis of flowering time in spring-type B. rapa, advancing early-maturity breeding efforts in crops.
{"title":"Map-based cloning and functional characterization reveal CDF3 as the causal gene for the flowering time phenotype in Brassica rapa and Brassica napus","authors":"Qianru Ma, Zhi Zhao, Kede Liu, Huaxin Li, Youjuan Quan, Long Wang, Hongping Zhao, Damei Pei, Guoyong Tang, Liang Xu, Lu Xiao, Dezhi Du","doi":"10.1093/hr/uhaf324","DOIUrl":"https://doi.org/10.1093/hr/uhaf324","url":null,"abstract":"Spring-type Brassica rapa L. is a valuable genetic resource for breeding early-maturing crops, offering advantages such as early flowering and rapid maturation. However, the genetic mechanisms governing flowering time (FT) in spring-type B. rapa remain insufficiently understood. In this study, we investigated the flowering-time trait of an extremely early-maturing landrace, “Haoyou 11”, originating from the Qinghai-Tibetan Plateau. Initial mapping was conducted using an F2 population derived from the cross between Haoyou 11 and Dahuang (a late-flowering spring-type landrace of B. rapa). A major quantitative trait locus (QTL) for flowering time, designated qFTA06, was identified within a 1.70 Mb interval on chromosome A06 using genotyping-by-sequencing (GBS) and bulked segregant analysis sequencing (BSA-seq). The locus qFTA06 was subsequently fine-mapped to a 75.16 kb region with a set of near-isogenic lines (NILs), and BrCDF3, a gene encoding a Dof transcription factor, was identified as the causal gene underlying qFTA06. Virus-induced gene silencing (VIGS) experiments revealed that BrCDF3 acts as a negative regulator of flowering time under long-day (LD) conditions, with sequence variation contributing to the early-flowering phenotype in Haoyou 11. Phenotypic analysis of NILs showed that NIL-E, carrying the BrCDF3 allele from Haoyou 11, flowered approximately 7 days earlier than NIL-L, which harbors the BrCDF3 allele from Dahuang. By employing CRISPR/Cas9 technology, we further validated that the homologous gene BnCDF3 also functions as a negative regulator of flowering time in Brassica napus L., and analyzed natural variations in the CDF3 gene across natural populations. This study provides new insights into the genetic basis of flowering time in spring-type B. rapa, advancing early-maturity breeding efforts in crops.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"151 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145609496","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}
Xiaodong Fu, Fujun Li, Yanan Li, Xiaoan Li, Xinhua Zhang, Zienab F R Ahmed
Low-temperature environments cause chilling injury in horticultural crops and accelerate quality deterioration after rewarming, which is closely related to epigenetic modifications. Epigenetic regulation is widely involved in various aspects of cold responses in horticultural crops, including the expression of cold-tolerant proteins, dynamic changes in cell membranes, energy metabolism, and reactive oxygen species metabolism. With the emergence and development of new scientific technologies, uncovering the secrets of epigenetic regulation in horticultural crops quality is becoming possible. Therefore, this paper reviews the types, roles, and potential mechanisms of epigenetic modifications involved in cold stress responses in horticultural crops, summarizes the dynamic changes and effects of exogenous treatments on epigenetic modifications, and discusses the feasibility of new editing technologies in epigenetic research and applications. This review aims to elucidate the complex regulatory mechanisms of epigenetic control in cold responses in horticultural crops, providing a theoretical foundation for developing novel strategies to control quality decline in horticultural crops.
{"title":"New insights in controlling horticultural crops quality deterioration caused by cold stress: epigenetic modification","authors":"Xiaodong Fu, Fujun Li, Yanan Li, Xiaoan Li, Xinhua Zhang, Zienab F R Ahmed","doi":"10.1093/hr/uhaf326","DOIUrl":"https://doi.org/10.1093/hr/uhaf326","url":null,"abstract":"Low-temperature environments cause chilling injury in horticultural crops and accelerate quality deterioration after rewarming, which is closely related to epigenetic modifications. Epigenetic regulation is widely involved in various aspects of cold responses in horticultural crops, including the expression of cold-tolerant proteins, dynamic changes in cell membranes, energy metabolism, and reactive oxygen species metabolism. With the emergence and development of new scientific technologies, uncovering the secrets of epigenetic regulation in horticultural crops quality is becoming possible. Therefore, this paper reviews the types, roles, and potential mechanisms of epigenetic modifications involved in cold stress responses in horticultural crops, summarizes the dynamic changes and effects of exogenous treatments on epigenetic modifications, and discusses the feasibility of new editing technologies in epigenetic research and applications. This review aims to elucidate the complex regulatory mechanisms of epigenetic control in cold responses in horticultural crops, providing a theoretical foundation for developing novel strategies to control quality decline in horticultural crops.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"1 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145609488","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}
Osmanthus fragrans is a well-known ornamental tree species for its pleasing floral fragrance. Linalool, as the characteristic aromatic component of O. fragrans, holds significant potential for applications in the flavor and fragrance industry. Although jasmonic acid (JA) is well-documented to regulate the biosynthesis and accumulation of various plant secondary metabolites, its role in linalool biosynthesis remains largely unclear. Here, we discovered a positive correlation between the endogenous JA levels and linalool accumulation during the flowering stage of O. fragrans. Exogenous JA treatment was shown to enhance linalool biosynthesis by activating the linalool synthase gene OfTPS2. Dual-LUC and EMSA assays demonstrated that the key protein in the JA signaling pathway, OfJAZ3, interacted with OfMYB21 and subsequently suppressed the transcriptional activation of OfTPS2 mediated by OfMYB21. Functional validation further revealed that overexpression of OfJAZ3 significantly inhibited linalool biosynthesis in O. fragrans, A. thaliana, and N. tabacum plants. In contrast, JA promoted the degradation of OfJAZ3, thereby disrupting the formation of the OfJAZ3-OfMYB21 complex and relieving its inhibitory effect on OfTPS2. Split-LUC, BiFC, and Pull-down assays confirmed that OfJAZ3 interacted with the F-box protein OfCOI1 (a key component of the E3 ubiquitin ligase SCFCOI1 complex), and JA treatment enhanced the strength of this interaction. Moreover, OfCOI1 was found to participate in OfTPS2 regulation by facilitating the ubiquitination and degradation of OfJAZ3. In conclusion, our findings elucidate the molecular mechanism by which OfJAZ3-OfMYB21 complex mediates JA signaling to regulate linalool biosynthesis in O. fragrans.
{"title":"The OfJAZ3-OfMYB21 complex mediates jasmonic acid signaling pathway to regulate linalool biosynthesis in Osmanthus fragrans","authors":"Yangang Lan, Xue Huang, Ziyi Li, Shunran Zhang, Yan Xiang, Hongbo Zhao","doi":"10.1093/hr/uhaf321","DOIUrl":"https://doi.org/10.1093/hr/uhaf321","url":null,"abstract":"Osmanthus fragrans is a well-known ornamental tree species for its pleasing floral fragrance. Linalool, as the characteristic aromatic component of O. fragrans, holds significant potential for applications in the flavor and fragrance industry. Although jasmonic acid (JA) is well-documented to regulate the biosynthesis and accumulation of various plant secondary metabolites, its role in linalool biosynthesis remains largely unclear. Here, we discovered a positive correlation between the endogenous JA levels and linalool accumulation during the flowering stage of O. fragrans. Exogenous JA treatment was shown to enhance linalool biosynthesis by activating the linalool synthase gene OfTPS2. Dual-LUC and EMSA assays demonstrated that the key protein in the JA signaling pathway, OfJAZ3, interacted with OfMYB21 and subsequently suppressed the transcriptional activation of OfTPS2 mediated by OfMYB21. Functional validation further revealed that overexpression of OfJAZ3 significantly inhibited linalool biosynthesis in O. fragrans, A. thaliana, and N. tabacum plants. In contrast, JA promoted the degradation of OfJAZ3, thereby disrupting the formation of the OfJAZ3-OfMYB21 complex and relieving its inhibitory effect on OfTPS2. Split-LUC, BiFC, and Pull-down assays confirmed that OfJAZ3 interacted with the F-box protein OfCOI1 (a key component of the E3 ubiquitin ligase SCFCOI1 complex), and JA treatment enhanced the strength of this interaction. Moreover, OfCOI1 was found to participate in OfTPS2 regulation by facilitating the ubiquitination and degradation of OfJAZ3. In conclusion, our findings elucidate the molecular mechanism by which OfJAZ3-OfMYB21 complex mediates JA signaling to regulate linalool biosynthesis in O. fragrans.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"1 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145594095","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}
Xiaoxu Li, Fang Li, Guo Wang, Shujun Wang, Xueren Cao, Ya Wu, Huanling Li, Jiabao Wang
Pericarp browning of postharvest litchi is a significant obstacle to the industry's high-quality development. Water loss from the pericarp is a key factor triggering browning, but the regulatory mechanism of water metabolism and its relationship with browning remain unclear. In this study, we found that aquaporin activity inhibitors (HgCl2) can delay both water loss and browning in litchi. LcPIP2;4, a PIP family member exhibiting high expression in the litchi pericarp and the greatest water transport activity, is significantly downregulated during water loss and browning. Further analysis revealed that HgCl₂ suppresses both the expression and water transport activity of LcPIP2;4, indicating a close association with the observed browning phenotype. By constructing transient overexpression fruits and transgenic callus tissues of LcPIP2;4 and measuring the water loss rate and browning index, we confirmed that LcPIP2;4 positively regulates water loss and browning in litchi. Through weighted gene co-expression network, LcPIP2;4 promoter sequence and qRT-PCR analysis, we identified 10 potential interacting transcription factors. Yeast one-hybrid, dual-luciferase reporter assay, chromatin immunoprecipitation analysis and electrophoretic mobility shift assay confirmed that LcMYB306 specifically binds to the LcPIP2;4 promoter. In LcMYB306 overexpressing fruits and embryogenic callus, LcPIP2;4 expression was suppressed, resulting in delayed water loss and browning. In contrast, in CRISPR/Cas9-edited LcMYB306 callus, LcPIP2;4 expression was upregulated, and water loss and browning were accelerated, confirming that LcMYB306 negatively regulates this process. This study demonstrates that LcMYB306 delays postharvest water loss and browning in litchi by repressing LcPIP2;4 transcriptionally expression. It provides a theoretical foundation and key target gene for developing litchi varieties resistant to browning.
{"title":"LcMYB306 regulates litchi fruit water loss and browning by inhibiting the expression of LcPIP2;4","authors":"Xiaoxu Li, Fang Li, Guo Wang, Shujun Wang, Xueren Cao, Ya Wu, Huanling Li, Jiabao Wang","doi":"10.1093/hr/uhaf322","DOIUrl":"https://doi.org/10.1093/hr/uhaf322","url":null,"abstract":"Pericarp browning of postharvest litchi is a significant obstacle to the industry's high-quality development. Water loss from the pericarp is a key factor triggering browning, but the regulatory mechanism of water metabolism and its relationship with browning remain unclear. In this study, we found that aquaporin activity inhibitors (HgCl2) can delay both water loss and browning in litchi. LcPIP2;4, a PIP family member exhibiting high expression in the litchi pericarp and the greatest water transport activity, is significantly downregulated during water loss and browning. Further analysis revealed that HgCl₂ suppresses both the expression and water transport activity of LcPIP2;4, indicating a close association with the observed browning phenotype. By constructing transient overexpression fruits and transgenic callus tissues of LcPIP2;4 and measuring the water loss rate and browning index, we confirmed that LcPIP2;4 positively regulates water loss and browning in litchi. Through weighted gene co-expression network, LcPIP2;4 promoter sequence and qRT-PCR analysis, we identified 10 potential interacting transcription factors. Yeast one-hybrid, dual-luciferase reporter assay, chromatin immunoprecipitation analysis and electrophoretic mobility shift assay confirmed that LcMYB306 specifically binds to the LcPIP2;4 promoter. In LcMYB306 overexpressing fruits and embryogenic callus, LcPIP2;4 expression was suppressed, resulting in delayed water loss and browning. In contrast, in CRISPR/Cas9-edited LcMYB306 callus, LcPIP2;4 expression was upregulated, and water loss and browning were accelerated, confirming that LcMYB306 negatively regulates this process. This study demonstrates that LcMYB306 delays postharvest water loss and browning in litchi by repressing LcPIP2;4 transcriptionally expression. It provides a theoretical foundation and key target gene for developing litchi varieties resistant to browning.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"104 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145559444","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}
Eggplant exhibits a diverse range of fruit colors, making it an excellent model for studying fruit pigmentation and its genetic regulation. While genes responsible for green and photosensitive purple fruit have been identified, the genetic basis of the non-photosensitive (NPS) fruit trait in eggplant has remained elusive. In this study, we characterized a major quantitative trait locus (QTL), SmNPS10.1, on chromosome 10 using QTL-seq. By combining linkage-based gene mapping with progeny testing, we fine-mapped SmNPS10.1 to a 33.58 kb interval, within which we identified SmMYB113, an R2R3-MYB transcription factor that regulates anthocyanin biosynthesis, as the candidate gene. Sequence analysis identified a unique 725-bp tandem repeat in the SmMYB113 promoter, present in four copies in NPS eggplant variety 21E27 but only a single copy in photosensitive varieties. This suggests that increased copy number of the repeat may drive light-independent expression of SmMYB113. Transgenic complementation confirmed the additional three copies of the 725-bp repeat in the promoter of SmMYB113 contributes to light-independent anthocyanin regulation. Additionally, we validated the KASP markers 21QP381 (linked to anthocyanin-present fruit color) and 23QP715 (linked to NPS fruit color) across multiple populations, providing powerful tools for marker-assisted selection in eggplant breeding. Our findings offer new insights into the molecular mechanisms controlling fruit color in eggplant and lay the groundwork for the development of molecular markers to facilitate breeding for NPS and other fruit color variants.
{"title":"A 725 bp quadruple repeat in the promoter of SmMYB113 is associated with light-independent anthocyanin regulation in eggplant","authors":"Zhilei Xia, Meng Yang, Yinggemei Huang, Bingxin Yu, Tingxia Wan, Duanhua Wang, Qian Li, Manoj Sapkota, Shuangshuang Yan, Bihao Cao, Zhengkun Qiu","doi":"10.1093/hr/uhaf319","DOIUrl":"https://doi.org/10.1093/hr/uhaf319","url":null,"abstract":"Eggplant exhibits a diverse range of fruit colors, making it an excellent model for studying fruit pigmentation and its genetic regulation. While genes responsible for green and photosensitive purple fruit have been identified, the genetic basis of the non-photosensitive (NPS) fruit trait in eggplant has remained elusive. In this study, we characterized a major quantitative trait locus (QTL), SmNPS10.1, on chromosome 10 using QTL-seq. By combining linkage-based gene mapping with progeny testing, we fine-mapped SmNPS10.1 to a 33.58 kb interval, within which we identified SmMYB113, an R2R3-MYB transcription factor that regulates anthocyanin biosynthesis, as the candidate gene. Sequence analysis identified a unique 725-bp tandem repeat in the SmMYB113 promoter, present in four copies in NPS eggplant variety 21E27 but only a single copy in photosensitive varieties. This suggests that increased copy number of the repeat may drive light-independent expression of SmMYB113. Transgenic complementation confirmed the additional three copies of the 725-bp repeat in the promoter of SmMYB113 contributes to light-independent anthocyanin regulation. Additionally, we validated the KASP markers 21QP381 (linked to anthocyanin-present fruit color) and 23QP715 (linked to NPS fruit color) across multiple populations, providing powerful tools for marker-assisted selection in eggplant breeding. Our findings offer new insights into the molecular mechanisms controlling fruit color in eggplant and lay the groundwork for the development of molecular markers to facilitate breeding for NPS and other fruit color variants.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"1 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145559445","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}
Drought stress significantly threatens tea production and quality worldwide. To elucidate the genetic basis of drought tolerance in tea plant, we evaluated 11 physiological traits across 115 diverse tea accessions under drought conditions. A comprehensive drought resistance index (D-value) was constructed through principal component analysis and fuzzy membership function. Genome-wide association studies (GWAS) identified 67 significant SNPs and pinpointed four candidate genes associated with drought-responsive traits. Integrated transcriptome and qRT-PCR analyses revealed that three genes, including CsAGD6, were significantly upregulated under drought stress. Functional assays confirmed that CsAGD6, encoding a nucleus-localized ARF-GAP protein, positively regulates drought tolerance by modulating photosynthetic efficiency and membrane stability. Haplotype analysis identified favorable alleles Hap-P1 and Hap-C1 in the promoter and coding regions of CsAGD6, respectively. Moreover, a SNP-KASP marker targeting chr10:206216541 (C/T) was developed and validated in 104 accessions, demonstrating high efficacy for early selection of drought-tolerant genotypes. This study provides novel insights into the molecular mechanisms of drought tolerance in tea plant and offers valuable genetic resources and tools for marker-assisted breeding.
{"title":"Genome-Wide Association Study and Functional Validation of CsAGD6 Conferring Drought Tolerance in Tea Plant","authors":"Jiaxuan Yue, Shan He, Shicai Liang, Yu Wang, Huan Wang, Xuxu Lang, Kai Fan, Jianhui Hu, Jiazhi Shen, Litao Sun, Shibo Ding, Zhaotang Ding, Wenjun Qian","doi":"10.1093/hr/uhaf320","DOIUrl":"https://doi.org/10.1093/hr/uhaf320","url":null,"abstract":"Drought stress significantly threatens tea production and quality worldwide. To elucidate the genetic basis of drought tolerance in tea plant, we evaluated 11 physiological traits across 115 diverse tea accessions under drought conditions. A comprehensive drought resistance index (D-value) was constructed through principal component analysis and fuzzy membership function. Genome-wide association studies (GWAS) identified 67 significant SNPs and pinpointed four candidate genes associated with drought-responsive traits. Integrated transcriptome and qRT-PCR analyses revealed that three genes, including CsAGD6, were significantly upregulated under drought stress. Functional assays confirmed that CsAGD6, encoding a nucleus-localized ARF-GAP protein, positively regulates drought tolerance by modulating photosynthetic efficiency and membrane stability. Haplotype analysis identified favorable alleles Hap-P1 and Hap-C1 in the promoter and coding regions of CsAGD6, respectively. Moreover, a SNP-KASP marker targeting chr10:206216541 (C/T) was developed and validated in 104 accessions, demonstrating high efficacy for early selection of drought-tolerant genotypes. This study provides novel insights into the molecular mechanisms of drought tolerance in tea plant and offers valuable genetic resources and tools for marker-assisted breeding.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"149 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145559446","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}
Vine tea (Nekemias grossedentata) is a dual-purpose medicinal and edible liana with a documented history of consumption in China spanning millennia. It has been extensively utilized among ethnic minority groups, including the Tujia, Yao, and Dong communities, for at least 700–1,000 years, where it is traditionally revered as the "Immortal Herb" or "Longevity Tea." This study reports the haplotype-resolved chromosome-scale genomes of two major cultivated diploid vine tea accessions (N. grossedentata, 2n = 40). Phylogenetic analysis revealed that N. grossedentata diverged from Cissus rotundifolia approximately 26.27 million years ago (MYA) and from Vitis vinifera around 17.30 MYA. Comparative genomic analysis within the genus uncovered species-specific evolutionary patterns. Furthermore, we constructed a pan-genome encompassing 39 vine tea cultivars and characterized structural variations among cultivated varieties. Correlation analysis between dihydromyricetin (DMY) content and leaf transcriptomes across these cultivars identified approximately 1 kb presence/absence variations (PAVs) associated with the expression of F3'5'H, a gene critical for DMY biosynthesis in vine tea. Collectively, this genomic resource provides a valuable foundation for advancing herbal crop breeding and development, while offering insights into the biosynthetic pathways underlying specialized metabolism in Vitaceae.
{"title":"Pan-genome assembly of Vine Tea ( Nekemias grossedentata ) reveals structural variation in its dihydromyricetin biosynthesis diversity","authors":"Danlu Han, Songyan Na, Zhuangwei Hou, Fangping Li, Chengluo Zhu, Yingying Li, Yingzi Zheng, Qiong Mo, Jiaqi Chen, Simin Xia, Xiaofan Zhou, Chengwei Yang, Jun Liu","doi":"10.1093/hr/uhaf307","DOIUrl":"https://doi.org/10.1093/hr/uhaf307","url":null,"abstract":"Vine tea (Nekemias grossedentata) is a dual-purpose medicinal and edible liana with a documented history of consumption in China spanning millennia. It has been extensively utilized among ethnic minority groups, including the Tujia, Yao, and Dong communities, for at least 700–1,000 years, where it is traditionally revered as the \"Immortal Herb\" or \"Longevity Tea.\" This study reports the haplotype-resolved chromosome-scale genomes of two major cultivated diploid vine tea accessions (N. grossedentata, 2n = 40). Phylogenetic analysis revealed that N. grossedentata diverged from Cissus rotundifolia approximately 26.27 million years ago (MYA) and from Vitis vinifera around 17.30 MYA. Comparative genomic analysis within the genus uncovered species-specific evolutionary patterns. Furthermore, we constructed a pan-genome encompassing 39 vine tea cultivars and characterized structural variations among cultivated varieties. Correlation analysis between dihydromyricetin (DMY) content and leaf transcriptomes across these cultivars identified approximately 1 kb presence/absence variations (PAVs) associated with the expression of F3'5'H, a gene critical for DMY biosynthesis in vine tea. Collectively, this genomic resource provides a valuable foundation for advancing herbal crop breeding and development, while offering insights into the biosynthetic pathways underlying specialized metabolism in Vitaceae.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"3 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145535809","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}
Anthurium, a highly diverse genus in the family Araceae, is well-known for its ornamental spathes and spadices. However, limited genomic resources hinder the study of floral traits and their evolutionary histories. Here, we present high-quality chromosome-level genome assemblies of Anthurium andraeanum and Anthurium scherzerianum. Comparative genomics revealed extensive chromosomal rearrangements and species-specific transposon expansions, which likely contributed to genome divergence. Two lineage-specific whole-genome duplications were identified, associated with gene family expansions linked to stress adaptation. Population structure analysis uncovered strong genetic admixture, reflecting widespread historical hybridization. Integrated transcriptomic and metabolomic analyses revealed dynamic regulatory networks governing spathe coloration through flavonoid–anthocyanin pathways. In addition, CER3, KCS1, and KCS3 were identified as key regulators involved in wax biosynthesis. Notably, inflorescence evolution correlates with the loss of the floral identity genes SOC1 and AGL6, highlighting conserved developmental pathways and lineage-specific innovations. Our findings provide foundational genomic resources for understanding Anthurium evolution, offer molecular targets for breeding programs, and elucidate transposon-driven genome expansion mechanisms that advance our knowledge of speciation in tropical epiphytes with exceptionally large genomes.
{"title":"Integrative multi-omics analysis reveals the genetic architecture of floral traits in Anthurium","authors":"Shengnan Lin, Chao Song, Dan Peng, Yaru Wang, Xiaoni Zhang, Yingxue Yang, Minlong Jia, Qingyun Leng, Shisong Xu, Xing’e Lin, Haiyan Li, Jinping Lu, Chengcheng Zhou, Xiao Wan, Jianrong Sun, Luke R Tembrock, Junmei Yin, Danqing Tian, Zhiqiang Wu, Junhai Niu","doi":"10.1093/hr/uhaf316","DOIUrl":"https://doi.org/10.1093/hr/uhaf316","url":null,"abstract":"Anthurium, a highly diverse genus in the family Araceae, is well-known for its ornamental spathes and spadices. However, limited genomic resources hinder the study of floral traits and their evolutionary histories. Here, we present high-quality chromosome-level genome assemblies of Anthurium andraeanum and Anthurium scherzerianum. Comparative genomics revealed extensive chromosomal rearrangements and species-specific transposon expansions, which likely contributed to genome divergence. Two lineage-specific whole-genome duplications were identified, associated with gene family expansions linked to stress adaptation. Population structure analysis uncovered strong genetic admixture, reflecting widespread historical hybridization. Integrated transcriptomic and metabolomic analyses revealed dynamic regulatory networks governing spathe coloration through flavonoid–anthocyanin pathways. In addition, CER3, KCS1, and KCS3 were identified as key regulators involved in wax biosynthesis. Notably, inflorescence evolution correlates with the loss of the floral identity genes SOC1 and AGL6, highlighting conserved developmental pathways and lineage-specific innovations. Our findings provide foundational genomic resources for understanding Anthurium evolution, offer molecular targets for breeding programs, and elucidate transposon-driven genome expansion mechanisms that advance our knowledge of speciation in tropical epiphytes with exceptionally large genomes.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"1 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145535810","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}
Yuhui Wang, Leo Gouaille, Jing Meng, Michael Nicolas, Laurent Ogé, Zhengrong Jiang, Laurent Crespel, Yanfeng Ding, José Le Gourrierec, Ganghua Li, Philippe Grappin, Soulaiman Sakr
Plants continuously integrate metabolic and hormonal signals to coordinate growth, development, and responses to environmental stimuli. Among these signals, sugars and strigolactones (SLs) have emerged as central regulators. Beyond serving as metabolic fuels, sugars act as signaling molecules that govern key developmental transitions and stress responses. SLs, a relatively recent addition to the phytohormone family, play pivotal roles in shaping plant architecture, modulating resource allocation, and facilitating environmental adaptation. While the individual signaling functions of sugars and SLs are well documented, their crosstalk remains an emerging and largely underexplored area of plant biology. This review synthesizes current knowledge on both the independent and interactive roles of sugar and SL signaling across critical developmental processes, including seed germination, hypocotyl elongation, root and shoot architecture, flowering, senescence and plant responses to abiotic and biotic stress. By analyzing antagonistic and synergistic interactions, we identify several potential integrative hubs where metabolic and hormonal signals converge to fine-tune the final decision. Notably, the nodal roles of BRC1 (BRANCHED1/TEOSINTE BRANCHED1), FT (FLOWERING LOCUS T), in mediating sugar–SL crosstalk in shoot branching, flowering, respectively, are highlighted. We also explore how sugar-SL interplay influences seed germination and plant adaptation to environmental stresses through shared regulators such as TOR (Target of Rapamycin) kinase, SnRK1 (Sucrose non-fermenting-1 Related Kinase 1), and SMXLs (Suppressor of MAX2-Like proteins). Understanding these interactions not only deepens our knowledge of fundamental plant biology but also offers new insights for improving the performance and resilience of crop and horticultural species.
{"title":"Decoding the sugar-strigolactone crosstalk: new frontier in plant growth and stress resilience","authors":"Yuhui Wang, Leo Gouaille, Jing Meng, Michael Nicolas, Laurent Ogé, Zhengrong Jiang, Laurent Crespel, Yanfeng Ding, José Le Gourrierec, Ganghua Li, Philippe Grappin, Soulaiman Sakr","doi":"10.1093/hr/uhaf278","DOIUrl":"https://doi.org/10.1093/hr/uhaf278","url":null,"abstract":"Plants continuously integrate metabolic and hormonal signals to coordinate growth, development, and responses to environmental stimuli. Among these signals, sugars and strigolactones (SLs) have emerged as central regulators. Beyond serving as metabolic fuels, sugars act as signaling molecules that govern key developmental transitions and stress responses. SLs, a relatively recent addition to the phytohormone family, play pivotal roles in shaping plant architecture, modulating resource allocation, and facilitating environmental adaptation. While the individual signaling functions of sugars and SLs are well documented, their crosstalk remains an emerging and largely underexplored area of plant biology. This review synthesizes current knowledge on both the independent and interactive roles of sugar and SL signaling across critical developmental processes, including seed germination, hypocotyl elongation, root and shoot architecture, flowering, senescence and plant responses to abiotic and biotic stress. By analyzing antagonistic and synergistic interactions, we identify several potential integrative hubs where metabolic and hormonal signals converge to fine-tune the final decision. Notably, the nodal roles of BRC1 (BRANCHED1/TEOSINTE BRANCHED1), FT (FLOWERING LOCUS T), in mediating sugar–SL crosstalk in shoot branching, flowering, respectively, are highlighted. We also explore how sugar-SL interplay influences seed germination and plant adaptation to environmental stresses through shared regulators such as TOR (Target of Rapamycin) kinase, SnRK1 (Sucrose non-fermenting-1 Related Kinase 1), and SMXLs (Suppressor of MAX2-Like proteins). Understanding these interactions not only deepens our knowledge of fundamental plant biology but also offers new insights for improving the performance and resilience of crop and horticultural species.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"186 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145545822","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}
Justin Joseph, Giorgio Perrella, Riccardo Aiese Cigliano, Marco di Marsico, Monica Canton, Esther Carrera, Lucio Conti, Claudio Bonghi, Serena Varotto
Bud dormancy in temperate perennials is often described as a stereotyped state of developmental repression triggered by environmental signals. Here, we investigate the development of vegetative buds in Prunus persica during the cold season to assess whether, like flower buds, they remain transcriptionally active. An integrated approach combining cytological analysis, hormone profiling, transcriptome sequencing, co-expression and gene regulatory network (GRN) inference, and in vivo interaction assays was used to compare bud types. Despite similar levels of abscisic acid and gibberellins during chilling accumulation, vegetative and flower buds displayed divergent transcriptional responses. Vegetative buds activated jasmonate- and photoperiod-responsive gene modules, while floral buds were marked by chilling-responsive modules regulated by SHORT VEGETATIVE PHASE 1 (SVP1). Bimolecular fluorescence complementation confirmed specific interactions between SVP1 and DORMANCY-ASSOCIATED MADS-box (DAM) proteins DAM3, DAM5, and DAM6. GRN analysis highlighted bud-specific combinations of DAM and SVP proteins, with DAM5 and DAM6 homodimers predominant in vegetative buds and DAM4 and SVP1/2 heterodimers dominant in flower buds. Our data revise the classical dormancy paradigm: flower and vegetative buds share hormonal trends yet deploy distinct MADS-box combinations to coordinate environment-dependent winter development. The organ-specific DAM/SVP circuitry uncovered here provides a new framework for mechanistic studies on cold mediated peach bud development.
{"title":"Beyond dormancy: organ-specific gene regulatory netw orks control winter development in peach buds","authors":"Justin Joseph, Giorgio Perrella, Riccardo Aiese Cigliano, Marco di Marsico, Monica Canton, Esther Carrera, Lucio Conti, Claudio Bonghi, Serena Varotto","doi":"10.1093/hr/uhaf310","DOIUrl":"https://doi.org/10.1093/hr/uhaf310","url":null,"abstract":"Bud dormancy in temperate perennials is often described as a stereotyped state of developmental repression triggered by environmental signals. Here, we investigate the development of vegetative buds in Prunus persica during the cold season to assess whether, like flower buds, they remain transcriptionally active. An integrated approach combining cytological analysis, hormone profiling, transcriptome sequencing, co-expression and gene regulatory network (GRN) inference, and in vivo interaction assays was used to compare bud types. Despite similar levels of abscisic acid and gibberellins during chilling accumulation, vegetative and flower buds displayed divergent transcriptional responses. Vegetative buds activated jasmonate- and photoperiod-responsive gene modules, while floral buds were marked by chilling-responsive modules regulated by SHORT VEGETATIVE PHASE 1 (SVP1). Bimolecular fluorescence complementation confirmed specific interactions between SVP1 and DORMANCY-ASSOCIATED MADS-box (DAM) proteins DAM3, DAM5, and DAM6. GRN analysis highlighted bud-specific combinations of DAM and SVP proteins, with DAM5 and DAM6 homodimers predominant in vegetative buds and DAM4 and SVP1/2 heterodimers dominant in flower buds. Our data revise the classical dormancy paradigm: flower and vegetative buds share hormonal trends yet deploy distinct MADS-box combinations to coordinate environment-dependent winter development. The organ-specific DAM/SVP circuitry uncovered here provides a new framework for mechanistic studies on cold mediated peach bud development.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"7 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145535812","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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