Ang Li, Mayila Yusuyin, Yuping Wei, Chengcheng Shen, Yushun Li, Yafei Li, Xiaoyan Hao, Mairebaike Muhamaitiha, Baike Wang, Juan Wang, Haiyan Lan, Bin Liu, Qinghui Yu
Drought stress profoundly impacts plant productivity worldwide. The roles of Basic helix–loop–helix (bHLH) transcription factors are critical in processes of plant growth, development, and stress management. However, roles of specific bHLH genes in tomato, particularly in relation to drought tolerance, remain poorly understood. This research identified SlbHLH70 as a factor that enhances drought tolerance in tomato. Transgenic lines overexpressing SlbHLH70 exhibited enhanced drought tolerance and improved post-stress recovery, whereas SlbHLH70 knockout mutants showed increased sensitivity to drought stress. Further study showed that SlbHLH70 directly regulated genes associated with abscisic acid (ABA) synthesis, ABA-mediated signal transduction, and root development. Our research identified SlbHLH70 as an important regulator of drought resistance in tomato, offering a valuable genetic target for enhancing crop resilience to water shortages.
{"title":"Transcription factor SlbHLH70 enhances drought tolerance in tomato","authors":"Ang Li, Mayila Yusuyin, Yuping Wei, Chengcheng Shen, Yushun Li, Yafei Li, Xiaoyan Hao, Mairebaike Muhamaitiha, Baike Wang, Juan Wang, Haiyan Lan, Bin Liu, Qinghui Yu","doi":"10.1093/hr/uhag075","DOIUrl":"https://doi.org/10.1093/hr/uhag075","url":null,"abstract":"Drought stress profoundly impacts plant productivity worldwide. The roles of Basic helix–loop–helix (bHLH) transcription factors are critical in processes of plant growth, development, and stress management. However, roles of specific bHLH genes in tomato, particularly in relation to drought tolerance, remain poorly understood. This research identified SlbHLH70 as a factor that enhances drought tolerance in tomato. Transgenic lines overexpressing SlbHLH70 exhibited enhanced drought tolerance and improved post-stress recovery, whereas SlbHLH70 knockout mutants showed increased sensitivity to drought stress. Further study showed that SlbHLH70 directly regulated genes associated with abscisic acid (ABA) synthesis, ABA-mediated signal transduction, and root development. Our research identified SlbHLH70 as an important regulator of drought resistance in tomato, offering a valuable genetic target for enhancing crop resilience to water shortages.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"90 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147360432","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}
Plasmopara viticola, the causal agent of grapevine downy mildew, exhibits substantial intraspecific variation in pathogenicity and genetic diversity, yet the genomic features underlying this variation remain incompletely characterized. Here, we sequenced and assembled two P. viticola isolates, PvH (from Vitis vinifera) and PvS (from V. amurensis), using PacBio HiFi sequencing, and performed comparative genomic analysis. Two complete genome assemblies (17 chromosomes) of P. viticola (PvH: 115.3 Mb; PvS: 113.0 Mb) were generated and revealed that nearly 90% of the putative effectors exist as local duplicated gene clusters. Comparative genomics uncovered distinct intraspecific expansion, deletion and diversification of putative effectors driven by local segmental, tandem, and proximal duplication events in P. viticola. Specifically, PvH exhibited a ~1.4-fold increase in CRNs (PvH: 237; PvS: 183; PV221: 169) and harbored 35 strain-specific CRNs. These differential effectors were predominantly clustered in complex structural variation hotspots (SVs, duplication and inversion). Notably, 104 putative effectors—including 21 RxLRs, 59 CRNs, and 24 CAZymes—located within inversion regions. Together, our results highlight a highly dynamic genome architecture in P. viticola, in which SV and local gene duplication are closely associated with effector diversification. This study provides a genome-resolved comparative framework for understanding intraspecific genomic diversity in P. viticola and establishes a foundation for future population-level and functional investigations.
{"title":"Complete genomes of grapevine downy mildew reveal effector cluster evolution driven by complex structural variations","authors":"Lianzhu Zhou, Shaowei Cui, Hao Zhang, Fanfang Kong, Qi Wang, Zhongyue Wang, Yongfeng Zhou, Shidong Li, Fei Du, Xiaoqing Huang, Yongqiang Liu","doi":"10.1093/hr/uhag073","DOIUrl":"https://doi.org/10.1093/hr/uhag073","url":null,"abstract":"Plasmopara viticola, the causal agent of grapevine downy mildew, exhibits substantial intraspecific variation in pathogenicity and genetic diversity, yet the genomic features underlying this variation remain incompletely characterized. Here, we sequenced and assembled two P. viticola isolates, PvH (from Vitis vinifera) and PvS (from V. amurensis), using PacBio HiFi sequencing, and performed comparative genomic analysis. Two complete genome assemblies (17 chromosomes) of P. viticola (PvH: 115.3 Mb; PvS: 113.0 Mb) were generated and revealed that nearly 90% of the putative effectors exist as local duplicated gene clusters. Comparative genomics uncovered distinct intraspecific expansion, deletion and diversification of putative effectors driven by local segmental, tandem, and proximal duplication events in P. viticola. Specifically, PvH exhibited a ~1.4-fold increase in CRNs (PvH: 237; PvS: 183; PV221: 169) and harbored 35 strain-specific CRNs. These differential effectors were predominantly clustered in complex structural variation hotspots (SVs, duplication and inversion). Notably, 104 putative effectors—including 21 RxLRs, 59 CRNs, and 24 CAZymes—located within inversion regions. Together, our results highlight a highly dynamic genome architecture in P. viticola, in which SV and local gene duplication are closely associated with effector diversification. This study provides a genome-resolved comparative framework for understanding intraspecific genomic diversity in P. viticola and establishes a foundation for future population-level and functional investigations.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"29 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147360379","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}
Chilling requirement (CR) is a key determinant for bud dormancy release in peach [Prunus persica (L.) Batsch]. To examine the genetic basis of CR and facilitate the breeding of climate-resilient varieties, we conducted a genome-wide association study (GWAS) on a diverse panel of 213 peach accessions with their CR phenotypes. The CR phenotypic data collected over three years demonstrated high heritability (H2 = 0.86), indicating a strong genetic component. The GWAS analysis identified 52 SNPs associated with CR traits, with major loci clustered on chromosome 1 (17.3–21.2 Mb and 43.7–47.3 Mb) and chromosome 2 (5.2–13.9 Mb), thereby both confirming established loci in the DAM cluster and identifying novel genetic regions. By focusing on regions exhibiting stable CR associations across years and which could be successfully validated by KASP assays, 13 candidate CR-related genes were identified. Two highly robust KASP markers derived from loci in chromosome 1 were developed and validated. These markers effectively discriminated between low (<400 h) and high (≥900 h) CR phenotypes. The combined use of these two markers achieved 95.5% accuracy in identifying extreme low-CR phenotypes (CR < 300 h) in peach accessions. The identification of genes linked to these robust markers of CR-related loci and the analysis of their expression during dormancy identified three potentially related with CR trait modulation: a receptor-like protein kinase, a protein kinase and a BED-type zinc finger domain-containing protein. This study provides useful molecular tools for marker-assisted breeding for low-CR peaches and new insights into the complex regulatory network of CR.
{"title":"Uncovering Novel Loci and Developing Functional KASP Markers for Chilling Requirement in Peach via GWAS","authors":"Juan Yan, Jianlan Xu, Jiyao Li, Zhixiang Cai, Zheng Chen, Binbin Zhang, Shaolei Guo, Yuanyuan Zhang, Lei Guo, Ruijuan Ma, Mingliang Yu, Zhijun Shen","doi":"10.1093/hr/uhag069","DOIUrl":"https://doi.org/10.1093/hr/uhag069","url":null,"abstract":"Chilling requirement (CR) is a key determinant for bud dormancy release in peach [Prunus persica (L.) Batsch]. To examine the genetic basis of CR and facilitate the breeding of climate-resilient varieties, we conducted a genome-wide association study (GWAS) on a diverse panel of 213 peach accessions with their CR phenotypes. The CR phenotypic data collected over three years demonstrated high heritability (H2 = 0.86), indicating a strong genetic component. The GWAS analysis identified 52 SNPs associated with CR traits, with major loci clustered on chromosome 1 (17.3–21.2 Mb and 43.7–47.3 Mb) and chromosome 2 (5.2–13.9 Mb), thereby both confirming established loci in the DAM cluster and identifying novel genetic regions. By focusing on regions exhibiting stable CR associations across years and which could be successfully validated by KASP assays, 13 candidate CR-related genes were identified. Two highly robust KASP markers derived from loci in chromosome 1 were developed and validated. These markers effectively discriminated between low (&lt;400 h) and high (≥900 h) CR phenotypes. The combined use of these two markers achieved 95.5% accuracy in identifying extreme low-CR phenotypes (CR &lt; 300 h) in peach accessions. The identification of genes linked to these robust markers of CR-related loci and the analysis of their expression during dormancy identified three potentially related with CR trait modulation: a receptor-like protein kinase, a protein kinase and a BED-type zinc finger domain-containing protein. This study provides useful molecular tools for marker-assisted breeding for low-CR peaches and new insights into the complex regulatory network of CR.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"29 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147360381","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}
Jia Guo, Xinyi Duan, He Xu, Zishan Xu, Alisdair R Fernie, Yanjie Zhang
Fruit and vegetable browning is a complex physiological phenomenon responsible for substantial postharvest losses and profound economic consequences. While enzymatic oxidation mediated by oxidative enzymes has long been considered the core mechanism, emerging evidence highlights the flavonoid pathway as an alternative route, influencing pigmentation outcomes. Browning is governed by a multi-tiered regulatory network spanning molecular, biochemical, cellular, and physiological levels, which encompasses transcriptional, post-transcriptional, epigenetic, and hormonal controls. Notably, regulatory mechanisms exhibit both conserved features and species-specific variations, reflecting potential adaptive evolution that may underlie differential browning responses across species. Here, we provide a thorough review of current advances in the mechanistic understanding of browning, with emphasis on providing evidence on multi-level regulations, identifying conserved mechanisms vs. species-specific variations, exploring their contributions to differential browning responses, and providing viable strategies for browning management through the application of exogenous hormones. Based on these, the current research landscape is critically assessed, and future research priorities are identified.
{"title":"Beyond a simple oxidation reaction: The complex molecular network regulating fruit and vegetable browning","authors":"Jia Guo, Xinyi Duan, He Xu, Zishan Xu, Alisdair R Fernie, Yanjie Zhang","doi":"10.1093/hr/uhag060","DOIUrl":"https://doi.org/10.1093/hr/uhag060","url":null,"abstract":"Fruit and vegetable browning is a complex physiological phenomenon responsible for substantial postharvest losses and profound economic consequences. While enzymatic oxidation mediated by oxidative enzymes has long been considered the core mechanism, emerging evidence highlights the flavonoid pathway as an alternative route, influencing pigmentation outcomes. Browning is governed by a multi-tiered regulatory network spanning molecular, biochemical, cellular, and physiological levels, which encompasses transcriptional, post-transcriptional, epigenetic, and hormonal controls. Notably, regulatory mechanisms exhibit both conserved features and species-specific variations, reflecting potential adaptive evolution that may underlie differential browning responses across species. Here, we provide a thorough review of current advances in the mechanistic understanding of browning, with emphasis on providing evidence on multi-level regulations, identifying conserved mechanisms vs. species-specific variations, exploring their contributions to differential browning responses, and providing viable strategies for browning management through the application of exogenous hormones. Based on these, the current research landscape is critically assessed, and future research priorities are identified.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"19 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147360433","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}
Tomato (Solanum lycopersicum) is a nutrient-rich and flavorful vegetable, ranking among the most consumed globally. In recent years, consumers have increasingly demanded high-quality tomatoes, prompting the extensive research into the key factors and relevant molecular mechanisms regulating the formation of fruit quality. Coloration is a crucial aspect determining the appearance quality of tomato fruits and directly affecting their commercial value. This coloration is intrinsically linked to the composition and abundance of special chemical compounds in fruits, particularly chlorophyll and carotenoids. Chlorophyll is the predominant pigment accumulated in the early stages of fruit development and plays a vital role in photosynthesis. As the fruit ripens, chlorophyll undergoes gradual degradation, while carotenoids are abundantly synthesized, resulting in a striking color transition from green to red. Chlorophyll and carotenoids are essential natural pigments and antioxidants that are indispensable for both coloration and nutritional value of tomato fruits. This review presents a comprehensive overview of the metabolic pathways and regulatory mechanisms of these metabolites, aiming to provide novel insights and strategies for improving tomato quality to meet the growing consumer demand for fruits with appealing coloration and enhanced nutrients.
{"title":"Metabolism and regulation of chlorophyll and carotenoids in tomato fruits","authors":"Weiqing Zhang, Ying Xie, Ying Yuan, Qian Long, Zhiyong Shao, Jirong Zheng, XueJuan Ru, Jia Luo, Guanghui Pan, Olubukola Oluranti Babalola, Wei Deng","doi":"10.1093/hr/uhag084","DOIUrl":"https://doi.org/10.1093/hr/uhag084","url":null,"abstract":"Tomato (Solanum lycopersicum) is a nutrient-rich and flavorful vegetable, ranking among the most consumed globally. In recent years, consumers have increasingly demanded high-quality tomatoes, prompting the extensive research into the key factors and relevant molecular mechanisms regulating the formation of fruit quality. Coloration is a crucial aspect determining the appearance quality of tomato fruits and directly affecting their commercial value. This coloration is intrinsically linked to the composition and abundance of special chemical compounds in fruits, particularly chlorophyll and carotenoids. Chlorophyll is the predominant pigment accumulated in the early stages of fruit development and plays a vital role in photosynthesis. As the fruit ripens, chlorophyll undergoes gradual degradation, while carotenoids are abundantly synthesized, resulting in a striking color transition from green to red. Chlorophyll and carotenoids are essential natural pigments and antioxidants that are indispensable for both coloration and nutritional value of tomato fruits. This review presents a comprehensive overview of the metabolic pathways and regulatory mechanisms of these metabolites, aiming to provide novel insights and strategies for improving tomato quality to meet the growing consumer demand for fruits with appealing coloration and enhanced nutrients.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"31 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147360382","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}
Safflower is featured with time-honored medical and economic values and developing into diverse phenotypic and genetic variations. In this study, to explore the critical genes associated with color phenotypes and flavonoid derivatives biosynthesis of safflower, BSA-seq, conflated with transcriptomic and metabolic methods were performed in two extreme colors (yellow and white) in the population of “ZHH0119” and “XHH007”. After crossing two parent plants reciprocally, the F4 generation of two accessions were used to construct near-isogenic gene pools for the two extreme traits of yellow and white safflower. BSA-seq results located five QTLs regions on chromosomes 2, 8, 9, 10 and 12 including six CtPALs, three CtC4Hs, two Ct4CLs, one CtCHS, thirty-two CtUGTs and seventy CtCYPs which tied to the yellow color phenotype of safflower. Through transcriptome analysis of two accessions and at different flowering stages, 1 CtPAL, 5 CtC4Hs, 4 CtCHSs, 3 CtCHIs, 3 CtFLSs, 48 CtUGTs, 51 CtCYPs and 75 transcription factors were revealed as significantly upregulated in the yellow accession compared to the white. Integrated analysis identified eight CtUGTs (CtUGT50-57) which exhibited significant positive correlations with chalcone glycosides of yellow safflower. Based on functional characterization, CtUGT52 was found to boost Hydroxysafflor yellow A (HSYA) content in yellow safflower which possessing substrate promiscuity (chalones, flavonols and flavonoids) and catalytic promiscuity (flavonols and flavonoids), revealing its vital role in the HSYA biosynthesis through transgenic overexpression. Combining catalytic mechanism verification of CtUGT52 towards phloretin, kaempferol and luteolin, our study to some extent, elucidated the modification function of CtUGTs for flavonoid aglycones in the flavonoid biosynthesis pathway of safflower.
红花具有悠久的药用和经济价值，并形成了多种表型和遗传变异。为了探索红花颜色表型和类黄酮衍生物生物合成相关的关键基因，本研究结合转录组学和代谢方法，对“ZHH0119”和“XHH007”两种极端颜色（黄色和白色）进行了BSA-seq分析。利用两份材料的F4代，对黄花和白花两种极端性状进行了近等基因基因库的构建。BSA-seq结果在2、8、9、10和12号染色体上定位了5个与红花黄色表型相关的qtl区域，包括6个ctpal、3个CtC4Hs、2个ct4cl、1个CtCHS、32个CtUGTs和70个CtCYPs。通过对两个品种和不同花期的转录组分析，发现1个CtPAL、5个CtC4Hs、4个CtCHSs、3个CtCHIs、3个CtFLSs、48个CtUGTs、51个CtCYPs和75个转录因子在黄色品种中显著上调。综合分析鉴定出8个CtUGTs （CtUGT50-57）与黄红花查尔酮苷呈显著正相关。基于功能表征，发现CtUGT52可提高黄红花中羟基afflor yellow A （HSYA）的含量，黄红花具有底物混杂性（chalones、黄酮醇和黄酮）和催化混杂性（黄酮醇和黄酮），揭示了其通过转基因过表达在HSYA生物合成中的重要作用。结合CtUGT52对根皮素、山奈酚和木犀草素的催化机理验证，我们的研究在一定程度上阐明了CtUGTs在红花类黄酮生物合成途径中对类黄酮苷元的修饰作用。
{"title":"BSA-seq Integrated with Transcriptomics and Metabolomics Revealing the Candidate Genes Associated with Safflower Colors and Flavonoid Glycosides Biosynthesis","authors":"Haotian Wang, Beixuan He, Shuyi Qi, Yue Gao, Xin Dong, Meili Guo","doi":"10.1093/hr/uhag068","DOIUrl":"https://doi.org/10.1093/hr/uhag068","url":null,"abstract":"Safflower is featured with time-honored medical and economic values and developing into diverse phenotypic and genetic variations. In this study, to explore the critical genes associated with color phenotypes and flavonoid derivatives biosynthesis of safflower, BSA-seq, conflated with transcriptomic and metabolic methods were performed in two extreme colors (yellow and white) in the population of “ZHH0119” and “XHH007”. After crossing two parent plants reciprocally, the F4 generation of two accessions were used to construct near-isogenic gene pools for the two extreme traits of yellow and white safflower. BSA-seq results located five QTLs regions on chromosomes 2, 8, 9, 10 and 12 including six CtPALs, three CtC4Hs, two Ct4CLs, one CtCHS, thirty-two CtUGTs and seventy CtCYPs which tied to the yellow color phenotype of safflower. Through transcriptome analysis of two accessions and at different flowering stages, 1 CtPAL, 5 CtC4Hs, 4 CtCHSs, 3 CtCHIs, 3 CtFLSs, 48 CtUGTs, 51 CtCYPs and 75 transcription factors were revealed as significantly upregulated in the yellow accession compared to the white. Integrated analysis identified eight CtUGTs (CtUGT50-57) which exhibited significant positive correlations with chalcone glycosides of yellow safflower. Based on functional characterization, CtUGT52 was found to boost Hydroxysafflor yellow A (HSYA) content in yellow safflower which possessing substrate promiscuity (chalones, flavonols and flavonoids) and catalytic promiscuity (flavonols and flavonoids), revealing its vital role in the HSYA biosynthesis through transgenic overexpression. Combining catalytic mechanism verification of CtUGT52 towards phloretin, kaempferol and luteolin, our study to some extent, elucidated the modification function of CtUGTs for flavonoid aglycones in the flavonoid biosynthesis pathway of safflower.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"272 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147360384","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}
Xuan Wang, Changyi Wang, Minkai Yang, Xiaohui Lai, Yile Sun, Tongming Yin, Bao Liu, Hansong Dong, Xiaobo Li, Zhonghao Ruan, Ju Huang, Aliya Fazal, Wencai Jie, Liu Yang, Xiaoran Lv, Hongwei Han, Dijun Chen, Guihua Lu, Sihai Yang, Zhongling Wen, Jinliang Qi, Yonghua Yang
Arnebia tschimganica is a vulnerable species within the Boraginaceae (Boraginales), has long been taxonomically debated due to inconsistent molecular and morphological characteristics. Shikonin and its derivatives, which are found in the roots of Boraginaceae species, possess significant pharmacological and industrial potential; however, the regulatory mechanisms underlying their biosynthesis are not yet fully comprehended. The lack of reference genomes for Arnebia species has hindered further research in these field. Here, this study sequenced and assembled the chromosome-level genome of A. tschimganica, revealing that Boraginales is sister to Lamiales within the Lamiids and suggesting the taxonomic status of A. tschimganica should be regressed from Arnebia to Lithospermum. A. tschimganica has undergone a recent whole-genome duplication that is shared with other Boraginaceae species, and this event has driven the evolution of shikonin biosynthesis. Multi-omics analysis revealed significant differences in shikonin production between A. tschimganica and L. erythrorhizon, attributing reduced shikonin productions in A. tschimganica to low transcript levels of key biosynthetic genes post-divergence. Furthermore, AtsDSH1, the enzyme responsible for catalyzing the hydroxylation of deoxyshikonin to shikonin in A. tschimganica, was identified and functionally characterized. Two ERF transcription factors were identified as conserved regulators of the dehydroshikonin hydroxylase gene DSH1, potentially regulating shikonin biosynthesis. These findings provide a chromosome-level genomic perspective to clarify the taxonomy of this controversial swing species and advance valuable insights for shikonin biosynthesis regulation.
{"title":"Genomics meets metabolomics: decoding Arnebia tschimganica and the shikonin biosynthesis pathway","authors":"Xuan Wang, Changyi Wang, Minkai Yang, Xiaohui Lai, Yile Sun, Tongming Yin, Bao Liu, Hansong Dong, Xiaobo Li, Zhonghao Ruan, Ju Huang, Aliya Fazal, Wencai Jie, Liu Yang, Xiaoran Lv, Hongwei Han, Dijun Chen, Guihua Lu, Sihai Yang, Zhongling Wen, Jinliang Qi, Yonghua Yang","doi":"10.1093/hr/uhag077","DOIUrl":"https://doi.org/10.1093/hr/uhag077","url":null,"abstract":"Arnebia tschimganica is a vulnerable species within the Boraginaceae (Boraginales), has long been taxonomically debated due to inconsistent molecular and morphological characteristics. Shikonin and its derivatives, which are found in the roots of Boraginaceae species, possess significant pharmacological and industrial potential; however, the regulatory mechanisms underlying their biosynthesis are not yet fully comprehended. The lack of reference genomes for Arnebia species has hindered further research in these field. Here, this study sequenced and assembled the chromosome-level genome of A. tschimganica, revealing that Boraginales is sister to Lamiales within the Lamiids and suggesting the taxonomic status of A. tschimganica should be regressed from Arnebia to Lithospermum. A. tschimganica has undergone a recent whole-genome duplication that is shared with other Boraginaceae species, and this event has driven the evolution of shikonin biosynthesis. Multi-omics analysis revealed significant differences in shikonin production between A. tschimganica and L. erythrorhizon, attributing reduced shikonin productions in A. tschimganica to low transcript levels of key biosynthetic genes post-divergence. Furthermore, AtsDSH1, the enzyme responsible for catalyzing the hydroxylation of deoxyshikonin to shikonin in A. tschimganica, was identified and functionally characterized. Two ERF transcription factors were identified as conserved regulators of the dehydroshikonin hydroxylase gene DSH1, potentially regulating shikonin biosynthesis. These findings provide a chromosome-level genomic perspective to clarify the taxonomy of this controversial swing species and advance valuable insights for shikonin biosynthesis regulation.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"5 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147360386","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}
Zhengyu Chen, Ziwei He, Juan Du, Yuhe Li, Siqi Niu, Aifang Ma, Qian Chen, Hailong Guo, Jun Fan, Maozhi Ren, Guangyuan Xu, Daolong Dou, Jinguang Yang, Maofeng Jing, Xiaodan Wang
Nucleotide-binding leucine-rich repeat receptors (NLRs) are central to plant immunity, yet the mechanisms regulating their homeostasis remain poorly understood. In this study, we identify StRWA2 as a susceptibility factor in potato (Solanum tuberosum) that negatively regulates NLR-mediated resistance to Phytophthora infestans. StRWA2 destabilizes NLR proteins R3a and Rpi-blb2 via the 26S proteasome, suppressing NLR-mediated hypersensitive responses (HR). Mechanistically, StRWA2 recruits the E3 ubiquitin ligase StSNIPER2 (SNC1-INFLUENCING PLANT E3 LIGASE REVERSE 2) and enhances its E3 ligase activity, enabling StSNIPER2-dependent ubiquitination and degradation of NLRs. Furthermore, we confirm the necessity of this partnership, which silencing NbSNIPER2a/b reduced StRWA2-mediated plant susceptibility, while expression of a ligase-dead StSNIPER2 variant (StSNIPER2H123Y) restored NLR stability and plant resistance. Crucially, we obtained StRWA2-silenced potato plants via the RNA interference (RNAi), which conferred resistance to P. infestans with no observable growth penalties compared to wild-type controls. Together, this study identified a susceptibility factor RWA2 from potato that recruits the E3 ligase SNIPER2 to destabilize NLRs. Our findings reveal a critical NLR regulation mode and propose RWA2 as a promising target for engineering disease resistance in crops.
{"title":"Potato RWA2 recruits the E3 ligase SNIPER2 to destabilize NLRs and promote Phytophthora infestans infection","authors":"Zhengyu Chen, Ziwei He, Juan Du, Yuhe Li, Siqi Niu, Aifang Ma, Qian Chen, Hailong Guo, Jun Fan, Maozhi Ren, Guangyuan Xu, Daolong Dou, Jinguang Yang, Maofeng Jing, Xiaodan Wang","doi":"10.1093/hr/uhag072","DOIUrl":"https://doi.org/10.1093/hr/uhag072","url":null,"abstract":"Nucleotide-binding leucine-rich repeat receptors (NLRs) are central to plant immunity, yet the mechanisms regulating their homeostasis remain poorly understood. In this study, we identify StRWA2 as a susceptibility factor in potato (Solanum tuberosum) that negatively regulates NLR-mediated resistance to Phytophthora infestans. StRWA2 destabilizes NLR proteins R3a and Rpi-blb2 via the 26S proteasome, suppressing NLR-mediated hypersensitive responses (HR). Mechanistically, StRWA2 recruits the E3 ubiquitin ligase StSNIPER2 (SNC1-INFLUENCING PLANT E3 LIGASE REVERSE 2) and enhances its E3 ligase activity, enabling StSNIPER2-dependent ubiquitination and degradation of NLRs. Furthermore, we confirm the necessity of this partnership, which silencing NbSNIPER2a/b reduced StRWA2-mediated plant susceptibility, while expression of a ligase-dead StSNIPER2 variant (StSNIPER2H123Y) restored NLR stability and plant resistance. Crucially, we obtained StRWA2-silenced potato plants via the RNA interference (RNAi), which conferred resistance to P. infestans with no observable growth penalties compared to wild-type controls. Together, this study identified a susceptibility factor RWA2 from potato that recruits the E3 ligase SNIPER2 to destabilize NLRs. Our findings reveal a critical NLR regulation mode and propose RWA2 as a promising target for engineering disease resistance in crops.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"54 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147360423","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}
Yi Chen, Sifei Duan, Meng Zhang, Yang-oujie Bao, Yungang Tian, Xuehui Dong, Min Ye
Astragalus membranaceus var. mongholicus (AMM) is the principal botanical source of Huangqi, a traditional medicinal herb whose therapeutic value primarily stems from the accumulation of isoflavones and other bioactive compounds in the roots. In this study, field surveys across major AMM production regions revealed pronounced natural variation in stem coloration. Chemical analysis showed that the roots of the red-stemmed type contained significantly higher levels of four bioactive isoflavones and volatile organic compounds than those in green-stemmed plants. Metabolomic profiling further revealed a specific enrichment of cyanidin-based anthocyanins in the red stems, establishing the metabolic basis of the red stem phenotype. Both transcriptomic and metabolomic analyses indicated an overall upregulation of the flavonoid and phenylpropanoid biosynthetic pathways in the stem and root tissues of red-stemmed AMM. Weighted gene co-expression network analysis (WGCNA) identified six key genes (AmC4H, AmCHS, AmCHI, AmF3H, AmF3′H, and AmBZ1) that were strongly associated with the red stem phenotype, all of which were specifically highly expressed in red stems. Functional assays confirmed their roles in anthocyanin biosynthesis. Molecular modeling provided further insights into the substrate specificity of AmBZ1. This study proposes stem color as a visible phenotypic reference for early-stage germplasm selection in AMM, and characterizes the molecular basis underlying red stem formation, providing a foundation for elite germplasm development and molecular breeding.
{"title":"Elucidating the Mechanisms Underlying Differential Anthocyanin Biosynthesis and Its Link to Stem Color and Root Isoflavonoid Levels in Astragalus membranaceus var. mongholicus","authors":"Yi Chen, Sifei Duan, Meng Zhang, Yang-oujie Bao, Yungang Tian, Xuehui Dong, Min Ye","doi":"10.1093/hr/uhag088","DOIUrl":"https://doi.org/10.1093/hr/uhag088","url":null,"abstract":"Astragalus membranaceus var. mongholicus (AMM) is the principal botanical source of Huangqi, a traditional medicinal herb whose therapeutic value primarily stems from the accumulation of isoflavones and other bioactive compounds in the roots. In this study, field surveys across major AMM production regions revealed pronounced natural variation in stem coloration. Chemical analysis showed that the roots of the red-stemmed type contained significantly higher levels of four bioactive isoflavones and volatile organic compounds than those in green-stemmed plants. Metabolomic profiling further revealed a specific enrichment of cyanidin-based anthocyanins in the red stems, establishing the metabolic basis of the red stem phenotype. Both transcriptomic and metabolomic analyses indicated an overall upregulation of the flavonoid and phenylpropanoid biosynthetic pathways in the stem and root tissues of red-stemmed AMM. Weighted gene co-expression network analysis (WGCNA) identified six key genes (AmC4H, AmCHS, AmCHI, AmF3H, AmF3′H, and AmBZ1) that were strongly associated with the red stem phenotype, all of which were specifically highly expressed in red stems. Functional assays confirmed their roles in anthocyanin biosynthesis. Molecular modeling provided further insights into the substrate specificity of AmBZ1. This study proposes stem color as a visible phenotypic reference for early-stage germplasm selection in AMM, and characterizes the molecular basis underlying red stem formation, providing a foundation for elite germplasm development and molecular breeding.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"11 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147360383","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}
Green flowers are uncommon in nature, yet they present a unique opportunity to explore the molecular, developmental, and evolutionary principles underlying floral pigmentation. While most species undergo petal degreening during maturation, some retain chlorophyll through suppressed degradation, sustained synthesis, or altered plastid differentiation. Here, we synthesize recent advances in understanding the molecular basis of green flower formation, integrating evidence from plastid biology, chlorophyll metabolism, transcription factor regulation, and floral organ identity genes. Research across diverse taxa reveals that chlorophyll homeostasis in petals is shaped by the interplay of light and hormonal signals, and orchestrated by transcriptional networks. In certain instances, homeotic transformations result in leaf-like characteristics. Naturally occurring variants, as well as engineered lines, offer powerful systems to dissect how developmental programs governing organ identity intersect with pigment metabolism. Green flowers also hold distinct ornamental and cultural value, expanding their relevance beyond ecological function. By tracing progress from morphological observations to multi-omics analyses, we highlight how this field is beginning to uncover shared regulatory frameworks and lineage-specific innovations. In the future, targeted manipulation of key regulatory nodes could enable the precise breeding of stable green blooms, while comparative studies promise deeper insights into how pigment pathways evolve and integrate with broader developmental networks. Understanding these processes will not only enrich floral biology but also enhance our ability to intentionally design and diversify plant phenotypes.
{"title":"Mechanisms underlying green flower formation","authors":"Xu Li, Conghao Hong, Hao Li, Sijia Hou, Qingqing Sun, Youyi Zang, Guorun Sun, Zhimin Huang, Hongbo Gao","doi":"10.1093/hr/uhag079","DOIUrl":"https://doi.org/10.1093/hr/uhag079","url":null,"abstract":"Green flowers are uncommon in nature, yet they present a unique opportunity to explore the molecular, developmental, and evolutionary principles underlying floral pigmentation. While most species undergo petal degreening during maturation, some retain chlorophyll through suppressed degradation, sustained synthesis, or altered plastid differentiation. Here, we synthesize recent advances in understanding the molecular basis of green flower formation, integrating evidence from plastid biology, chlorophyll metabolism, transcription factor regulation, and floral organ identity genes. Research across diverse taxa reveals that chlorophyll homeostasis in petals is shaped by the interplay of light and hormonal signals, and orchestrated by transcriptional networks. In certain instances, homeotic transformations result in leaf-like characteristics. Naturally occurring variants, as well as engineered lines, offer powerful systems to dissect how developmental programs governing organ identity intersect with pigment metabolism. Green flowers also hold distinct ornamental and cultural value, expanding their relevance beyond ecological function. By tracing progress from morphological observations to multi-omics analyses, we highlight how this field is beginning to uncover shared regulatory frameworks and lineage-specific innovations. In the future, targeted manipulation of key regulatory nodes could enable the precise breeding of stable green blooms, while comparative studies promise deeper insights into how pigment pathways evolve and integrate with broader developmental networks. Understanding these processes will not only enrich floral biology but also enhance our ability to intentionally design and diversify plant phenotypes.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"32 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147360385","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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