Rui Xia, Lin Chen, Pengfei Wang, Baoying Huang, Baoling Liang, Shengzhe Lin, Guangsheng Yang, Dengfeng Hong
Flower color is a key trait influencing insect pollination and ornamental value, yet the molecular mechanisms underlying heterozygous flower color remain unclear. In this study, we identified the creation of a yellow-white chimeric flower (cf) mutation in Brassica napus, characterized as the coexistence of yellow and white colors on petals of the same flower. Genetic analysis revealed that chimeric flower formation is controlled by a completely dominant gene. Map-based cloning, transgenic complementation, and CRISPR/Cas9 experiments consistently confirmed that BnaC05G0385300ZS on chromosome C05 is the causal gene of CF, which encodes a plastid DNA polymerase IB (BnaC05.POLIB). A G-to-A mutation in the seventh exon results in a D742N substitution, which disrupts Mg2+ binding and impairs polymerase activity. This leads to a reduced plastid genome copy number, decreased chromoplast formation, and aberrant carotenoid accumulation, ultimately resulting in the chimeric phenotype in a dosage-dependent manner. These findings reveal a novel role for BnaC05.POLIB in petal color patterning and provide a strategy for breeding ornamental plants with heterozygous flowers.
{"title":"A single nucleotide mutation of BnaC05.POLIB creates yellow-white chimeric flower in Brassica napus","authors":"Rui Xia, Lin Chen, Pengfei Wang, Baoying Huang, Baoling Liang, Shengzhe Lin, Guangsheng Yang, Dengfeng Hong","doi":"10.1093/hr/uhaf276","DOIUrl":"https://doi.org/10.1093/hr/uhaf276","url":null,"abstract":"Flower color is a key trait influencing insect pollination and ornamental value, yet the molecular mechanisms underlying heterozygous flower color remain unclear. In this study, we identified the creation of a yellow-white chimeric flower (cf) mutation in Brassica napus, characterized as the coexistence of yellow and white colors on petals of the same flower. Genetic analysis revealed that chimeric flower formation is controlled by a completely dominant gene. Map-based cloning, transgenic complementation, and CRISPR/Cas9 experiments consistently confirmed that BnaC05G0385300ZS on chromosome C05 is the causal gene of CF, which encodes a plastid DNA polymerase IB (BnaC05.POLIB). A G-to-A mutation in the seventh exon results in a D742N substitution, which disrupts Mg2+ binding and impairs polymerase activity. This leads to a reduced plastid genome copy number, decreased chromoplast formation, and aberrant carotenoid accumulation, ultimately resulting in the chimeric phenotype in a dosage-dependent manner. These findings reveal a novel role for BnaC05.POLIB in petal color patterning and provide a strategy for breeding ornamental plants with heterozygous flowers.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"48 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146169510","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}
In the context of global warming, elevated temperatures present serious challenges to the growth, quality, and productivity of nonheading Chinese cabbage (NHCC). Understanding the mechanisms underlying thermotolerance in NHCCs is therefore critically important. In this study, we investigated the influence of heat stress (HS) duration and circadian rhythm on gene expression using time-resolved transcriptome sequencing. The results showed that during the early stages of HS, NHCC primarily engaged in physiological processes such as stimulus perception and signal transduction. In contrast, prolonged HS exposure activated antioxidant metabolism, reduced photosynthetic capacity, and accelerated leaf senescence. Weighted gene co-expression network analysis (WGCNA) further revealed a strong link between circadian regulation and HS responses. Notably, our findings demonstrate that the core circadian clock component CIRCADIAN CLOCK ASSOCIATED 1 (BcCCA1) negatively regulated heat tolerance by repressing the transcription of BcHSFA2. Collectively, these results provide new insights into the molecular mechanisms underlying HS responses in NHCCs and highlight the regulatory role of circadian rhythms in plant thermotolerance.
{"title":"CIRCADIAN CLOCK ASSOCIATED 1 represses thermotolerance by inhibiting HEAT SHOCK FACTOR A2 expression in nonheading Chinese cabbage","authors":"Ying He, Dong Xiao, Xlin Hou, Yiran Li, Hongfang Zhu","doi":"10.1093/hr/uhag033","DOIUrl":"https://doi.org/10.1093/hr/uhag033","url":null,"abstract":"In the context of global warming, elevated temperatures present serious challenges to the growth, quality, and productivity of nonheading Chinese cabbage (NHCC). Understanding the mechanisms underlying thermotolerance in NHCCs is therefore critically important. In this study, we investigated the influence of heat stress (HS) duration and circadian rhythm on gene expression using time-resolved transcriptome sequencing. The results showed that during the early stages of HS, NHCC primarily engaged in physiological processes such as stimulus perception and signal transduction. In contrast, prolonged HS exposure activated antioxidant metabolism, reduced photosynthetic capacity, and accelerated leaf senescence. Weighted gene co-expression network analysis (WGCNA) further revealed a strong link between circadian regulation and HS responses. Notably, our findings demonstrate that the core circadian clock component CIRCADIAN CLOCK ASSOCIATED 1 (BcCCA1) negatively regulated heat tolerance by repressing the transcription of BcHSFA2. Collectively, these results provide new insights into the molecular mechanisms underlying HS responses in NHCCs and highlight the regulatory role of circadian rhythms in plant thermotolerance.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"60 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146161077","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}
Meiqi Zhou, Yilin Wang, Kim Lien Phan Thi, Yao Chi, Xu Li, Yang Li, Chao Wang
This research examines how the basic leucine zipper (bZIP) transcription factor (TF) influences drought stress responses in tree species, emphasizing its related regulatory pathways, and thus offering a theoretical framework for understanding drought response mechanisms regulated by the bZIP TF family. Specifically, we characterized the functional role of the S subfamily bZIP gene, PtrbZIP12, from Populus trichocarpa, by developing transgenic poplars that either overexpressed or knocked down of PtrbZIP12. The findings indicated that PtrbZIP12 markedly improved drought tolerance in transgenic plants by facilitating reactive oxygen species (ROS) scavenging, enhancing proline biosynthesis, and reducing plasma membrane peroxidation and cell death. To pinpoint PtrbZIP12’s downstream targets, RNA sequencing was performed, followed by chromatin immunoprecipitation-PCR (ChIP-PCR), yeast one-hybrid, and dual-luciferase assays. These analyses confirmed that PtrbZIP12 binds directly to the promoters of PtrDHN (Dehydrin) and PtrPOD (peroxidase), leading to the activation of their expression. Transgenic poplars overexpressing (OE) PtrDHN or PtrPOD were subsequently generated, and similar to PtrbZIP12, their OE conferred enhanced drought tolerance. Moreover, co-expression of PtrbZIP12 with PtrbZIP3 further elevated PtrDHN transcript levels, resulting in improved drought resilience in the PtrbZIP12 transgenic lines. Moreover, phosphorylation was identified as a key factor in boosting PtrbZIP12-mediated transcriptional regulation of PtrPOD and PtrDHN, underscoring the significance of post-translational modification in plant drought stress responses.
{"title":"PtrbZIP12 improves drought resistance in Populus trichocarpa by directly targeting PtrDHN and PtrPOD","authors":"Meiqi Zhou, Yilin Wang, Kim Lien Phan Thi, Yao Chi, Xu Li, Yang Li, Chao Wang","doi":"10.1093/hr/uhag034","DOIUrl":"https://doi.org/10.1093/hr/uhag034","url":null,"abstract":"This research examines how the basic leucine zipper (bZIP) transcription factor (TF) influences drought stress responses in tree species, emphasizing its related regulatory pathways, and thus offering a theoretical framework for understanding drought response mechanisms regulated by the bZIP TF family. Specifically, we characterized the functional role of the S subfamily bZIP gene, PtrbZIP12, from Populus trichocarpa, by developing transgenic poplars that either overexpressed or knocked down of PtrbZIP12. The findings indicated that PtrbZIP12 markedly improved drought tolerance in transgenic plants by facilitating reactive oxygen species (ROS) scavenging, enhancing proline biosynthesis, and reducing plasma membrane peroxidation and cell death. To pinpoint PtrbZIP12’s downstream targets, RNA sequencing was performed, followed by chromatin immunoprecipitation-PCR (ChIP-PCR), yeast one-hybrid, and dual-luciferase assays. These analyses confirmed that PtrbZIP12 binds directly to the promoters of PtrDHN (Dehydrin) and PtrPOD (peroxidase), leading to the activation of their expression. Transgenic poplars overexpressing (OE) PtrDHN or PtrPOD were subsequently generated, and similar to PtrbZIP12, their OE conferred enhanced drought tolerance. Moreover, co-expression of PtrbZIP12 with PtrbZIP3 further elevated PtrDHN transcript levels, resulting in improved drought resilience in the PtrbZIP12 transgenic lines. Moreover, phosphorylation was identified as a key factor in boosting PtrbZIP12-mediated transcriptional regulation of PtrPOD and PtrDHN, underscoring the significance of post-translational modification in plant drought stress responses.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"40 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146122168","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}
Elevated atmospheric [CO2] and nitrogen (N) availability are critical determinants of plants growth. This study investigated the underlying mechanisms of hormone in mediating elevated [CO2]-promoted shoot growth and leaf elongation under different N conditions in tall fescue (Festuca arundinacea). Plants were grown under low N (LN, 0.25 mM) and moderate N (MN, 4 mM) conditions. Subsequently, the plants from each N treatment were divided and immediately transferred to ambient (400 μmol·mol−1) or elevated [CO2] (800 μmol·mol−1), respectively. Elevated [CO2] promoted plant growth under both LN and MN conditions through affecting cell division and cell elongation, with a more pronounced effect under MN supply levels. Elevated [CO2]-induced shoot growth and leaf elongation were associated with increased cytokinin level under LN and with enhanced both cytokinin and auxin under MN conditions. Exogenous cytokinin inhibitor (lovastatin) and auxin inhibitor (2,3,5-triiodobenzoic) altered elevated [CO2]-enhanced growth on tall fescue regardless of N conditions. Elevated [CO2]-enhanced growth by modulating cell growth-related genes OsCycD2, OsPCNA, and OsEXPA10 was counteracted and reduced in FaCKX11-OE lines under LN and MN conditions, respectively. However, this enhancement was counteracted in FaDAO-OE lines under MN but not under LN conditions. These results demonstrated that elevated [CO2]-enhanced shoot growth in perennial grass species could be primarily mediated by cytokinin under LN conditions, while both cytokinin and auxin were involved in regulating elevated [CO2]-enhanced growth under MN conditions.
{"title":"Cytokinin and Auxin Metabolism Mediation of Elevated [CO2]-Enhanced Shoot Growth under Different Nitrogen Conditions in Perennial Grass","authors":"Ningli Fan, Qiuguo Li, Tian Hao, Danyi Wang, Peishuang Yang, Jingjin Yu, Zhimin Yang","doi":"10.1093/hr/uhag025","DOIUrl":"https://doi.org/10.1093/hr/uhag025","url":null,"abstract":"Elevated atmospheric [CO2] and nitrogen (N) availability are critical determinants of plants growth. This study investigated the underlying mechanisms of hormone in mediating elevated [CO2]-promoted shoot growth and leaf elongation under different N conditions in tall fescue (Festuca arundinacea). Plants were grown under low N (LN, 0.25 mM) and moderate N (MN, 4 mM) conditions. Subsequently, the plants from each N treatment were divided and immediately transferred to ambient (400 μmol·mol−1) or elevated [CO2] (800 μmol·mol−1), respectively. Elevated [CO2] promoted plant growth under both LN and MN conditions through affecting cell division and cell elongation, with a more pronounced effect under MN supply levels. Elevated [CO2]-induced shoot growth and leaf elongation were associated with increased cytokinin level under LN and with enhanced both cytokinin and auxin under MN conditions. Exogenous cytokinin inhibitor (lovastatin) and auxin inhibitor (2,3,5-triiodobenzoic) altered elevated [CO2]-enhanced growth on tall fescue regardless of N conditions. Elevated [CO2]-enhanced growth by modulating cell growth-related genes OsCycD2, OsPCNA, and OsEXPA10 was counteracted and reduced in FaCKX11-OE lines under LN and MN conditions, respectively. However, this enhancement was counteracted in FaDAO-OE lines under MN but not under LN conditions. These results demonstrated that elevated [CO2]-enhanced shoot growth in perennial grass species could be primarily mediated by cytokinin under LN conditions, while both cytokinin and auxin were involved in regulating elevated [CO2]-enhanced growth under MN conditions.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"99 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146101325","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}
Yuchao Tang, Bohao Tan, Huiyu Liu, Yijie Liu, Lu Zhang, Peng Zhang, Ming Sun
Global climate change and widespread unsustainable agricultural practices, increasingly impose both biotic and abiotic stresses on the production of horticultural plants. Lilies (Lilium spp.) are globally renowned ornamental plants, with some species also possessing medicinal, edible, and cosmetic value. However, their quality and yield are often negatively affected by various stresses. Conventional breeding methods are often inefficient due to the long juvenile phase, complex genetic background, and large genome size of lilies. While numerous emerging technologies provide opportunities for resistance breeding in lilies, their successful application relies on a thorough understanding of the resistance response mechanisms. This review systematically summarizes recent advances in lily stress resistance research, delineates the physiological and molecular response mechanisms of lilies under abiotic stresses (extreme temperature, drought, high salinity), biotic stresses (pathogens, pests), and continuous cropping obstacles. Furthermore, it discusses current challenges and limitations, and explores the potential applications of emerging technologies in improving the stress adaptability of lilies. These findings provide important insights for advancing stress resistance research and breeding stress-tolerant lily cultivars.
{"title":"A comprehensive review of physiological and molecular responses to stress of lilies (genus Lilium )","authors":"Yuchao Tang, Bohao Tan, Huiyu Liu, Yijie Liu, Lu Zhang, Peng Zhang, Ming Sun","doi":"10.1093/hr/uhaf347","DOIUrl":"https://doi.org/10.1093/hr/uhaf347","url":null,"abstract":"Global climate change and widespread unsustainable agricultural practices, increasingly impose both biotic and abiotic stresses on the production of horticultural plants. Lilies (Lilium spp.) are globally renowned ornamental plants, with some species also possessing medicinal, edible, and cosmetic value. However, their quality and yield are often negatively affected by various stresses. Conventional breeding methods are often inefficient due to the long juvenile phase, complex genetic background, and large genome size of lilies. While numerous emerging technologies provide opportunities for resistance breeding in lilies, their successful application relies on a thorough understanding of the resistance response mechanisms. This review systematically summarizes recent advances in lily stress resistance research, delineates the physiological and molecular response mechanisms of lilies under abiotic stresses (extreme temperature, drought, high salinity), biotic stresses (pathogens, pests), and continuous cropping obstacles. Furthermore, it discusses current challenges and limitations, and explores the potential applications of emerging technologies in improving the stress adaptability of lilies. These findings provide important insights for advancing stress resistance research and breeding stress-tolerant lily cultivars.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"8 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146098265","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}
Malik Umair Faiz, Xin Liu, Jiarui Sun, Cecilia H Deng, Yanfei Liu, Xinxin Wang, Zihan Fan, Xueying Hong, Lihuan Wang, Wei Li, Wei Tang, Pu Liu, Yang Song, Xiujuan Qi, Dawei Li, Xueren Yin, Yongsheng Liu, Junyang Yue
Kiwifruit (Actinidia spp.) is a globally significant horticultural crop, renowned for its exceptional nutritional value and high vitamin C content. The distinctive genetic features of this genus, including a dioecious sexual system (XY/XX) and a wide range of ploidy (2x–10x), have driven substantial genomic and phenotypic diversification, thereby constituting a valuable germplasm resource for systematic breeding. Recent advances in kiwifruit genomics are transforming the field and revolutionizing our understanding of its evolution, domestication, and the genetic mechanisms underlying agronomic traits. In this review, we highlight the key achievements in kiwifruit genome research over the past decades, chronologically spanning from the initial draft genome assembly to the recent super pan-genome construction. We further synthesize how multi-omics approaches have been leveraged for fine mapping, gene discovery, and the analysis of gene expression and metabolic pathways. Finally, we discuss future research directions and breeding strategies enabled by these genomic breakthroughs, particularly through the applications of genomic selection and gene editing in kiwifruit.
{"title":"Kiwifruit genomics and applications: recent advances, current challenges and future prospects","authors":"Malik Umair Faiz, Xin Liu, Jiarui Sun, Cecilia H Deng, Yanfei Liu, Xinxin Wang, Zihan Fan, Xueying Hong, Lihuan Wang, Wei Li, Wei Tang, Pu Liu, Yang Song, Xiujuan Qi, Dawei Li, Xueren Yin, Yongsheng Liu, Junyang Yue","doi":"10.1093/hr/uhag024","DOIUrl":"https://doi.org/10.1093/hr/uhag024","url":null,"abstract":"Kiwifruit (Actinidia spp.) is a globally significant horticultural crop, renowned for its exceptional nutritional value and high vitamin C content. The distinctive genetic features of this genus, including a dioecious sexual system (XY/XX) and a wide range of ploidy (2x–10x), have driven substantial genomic and phenotypic diversification, thereby constituting a valuable germplasm resource for systematic breeding. Recent advances in kiwifruit genomics are transforming the field and revolutionizing our understanding of its evolution, domestication, and the genetic mechanisms underlying agronomic traits. In this review, we highlight the key achievements in kiwifruit genome research over the past decades, chronologically spanning from the initial draft genome assembly to the recent super pan-genome construction. We further synthesize how multi-omics approaches have been leveraged for fine mapping, gene discovery, and the analysis of gene expression and metabolic pathways. Finally, we discuss future research directions and breeding strategies enabled by these genomic breakthroughs, particularly through the applications of genomic selection and gene editing in kiwifruit.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"297 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146071657","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}
Lei Zhao, Di Ai, Zhaoyang Li, Miaoyi Li, Chaoxi Luo, Qian Peng, Yuepeng Han, Jian-Ping An
Bacterial spot (BS) disease significantly impairs vigor, fruit quality, and yield in peach trees. However, research on this disease remains limited. In this study, peach leaves and fruits were inoculated with the pathogen isolated from infected leaves, triggering a robust accumulation of proanthocyanidins (PA) in both tissues. Further investigation revealed that pathogen inoculation promoted PA accumulation by upregulating PpMYB123, which transactivated the core PA biosynthetic genes PpANR and PpLAR. Notably, the E3 ubiquitin ligase PpPUB23 negatively regulated PpMYB123. However, its transcript levels were significantly suppressed following inoculation, thereby stabilizing PpMYB123 and enhancing PA production. PA conferred dual protection by scavenging excess reactive oxygen species (ROS) and suppressing pathogen growth. Our findings provide molecular evidence for PA-mediated defense against BS disease in peach.
{"title":"PpMYB123 -mediated proanthocyanidin accumulation alleviates bacterial spot disease in peach","authors":"Lei Zhao, Di Ai, Zhaoyang Li, Miaoyi Li, Chaoxi Luo, Qian Peng, Yuepeng Han, Jian-Ping An","doi":"10.1093/hr/uhag032","DOIUrl":"https://doi.org/10.1093/hr/uhag032","url":null,"abstract":"Bacterial spot (BS) disease significantly impairs vigor, fruit quality, and yield in peach trees. However, research on this disease remains limited. In this study, peach leaves and fruits were inoculated with the pathogen isolated from infected leaves, triggering a robust accumulation of proanthocyanidins (PA) in both tissues. Further investigation revealed that pathogen inoculation promoted PA accumulation by upregulating PpMYB123, which transactivated the core PA biosynthetic genes PpANR and PpLAR. Notably, the E3 ubiquitin ligase PpPUB23 negatively regulated PpMYB123. However, its transcript levels were significantly suppressed following inoculation, thereby stabilizing PpMYB123 and enhancing PA production. PA conferred dual protection by scavenging excess reactive oxygen species (ROS) and suppressing pathogen growth. Our findings provide molecular evidence for PA-mediated defense against BS disease in peach.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"86 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146071658","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}
Crotalaria is a genus of the Fabaceae family with agricultural and medicinal value, but to date the genome has not been fully sequenced. Although Crotalaria pallida is widely distributed in tropical and subtropical regions, the degree of genetic diversity and the specific traits influenced by geographic dispersal remain unknown. We here report a high-quality genome assembly of C. pallida with 98.52% coverage which is assembled into 8 chromosomes. C. pallida is closely related to Lupinus angustifolius, with genetic divergence occurring approximately 42.5-57.4 million years ago (MYA). Re-sequencing of 236 C. pallida accessions revealed a genetic diversity decrease as C. pallida spread from Africa to America and Asia, and from Asia to China and finally to Hainan. Significant divergence was observed in seven traits between non-Hainan and Hainan accessions. Genome-wide association studies identified 73 loci for 18 agronomic traits, 25 of which overlapped with divergent sweeps between non-Hainan accessions and Hainan accessions. Furthermore, the dispersal of C. pallida in Hainan reduced genetic diversity, leading to a divergence in allelic frequencies at four candidate genes (CpPTR, CpMYB, CpRLPK, and CpNADK) associated with plant height. This study reveals the genetic basis of trait divergence driven by geographic dispersal and offers valuable resources for the strategic development of C. pallida breeding.
{"title":"High-quality genome and variation map reveal valuable loci and the genetic basis of trait divergence driven by geographic dispersal in Crotalaria pallida","authors":"Hubiao Yang, Xiaoxue Ye, Yiming Wang, Wei Yan, Changmian Ji, Yu Wang, Zehong Ding, Weiwei Tie, Fei Yan, Zhenfan Hao, Qian Liu, Zhengyang Zhong, Xuekui Dong, Ling Kang, Mufei Zhu, Hao Lv, Wei Hu, Guodao Liu, Zhibiao Nan","doi":"10.1093/hr/uhag026","DOIUrl":"https://doi.org/10.1093/hr/uhag026","url":null,"abstract":"Crotalaria is a genus of the Fabaceae family with agricultural and medicinal value, but to date the genome has not been fully sequenced. Although Crotalaria pallida is widely distributed in tropical and subtropical regions, the degree of genetic diversity and the specific traits influenced by geographic dispersal remain unknown. We here report a high-quality genome assembly of C. pallida with 98.52% coverage which is assembled into 8 chromosomes. C. pallida is closely related to Lupinus angustifolius, with genetic divergence occurring approximately 42.5-57.4 million years ago (MYA). Re-sequencing of 236 C. pallida accessions revealed a genetic diversity decrease as C. pallida spread from Africa to America and Asia, and from Asia to China and finally to Hainan. Significant divergence was observed in seven traits between non-Hainan and Hainan accessions. Genome-wide association studies identified 73 loci for 18 agronomic traits, 25 of which overlapped with divergent sweeps between non-Hainan accessions and Hainan accessions. Furthermore, the dispersal of C. pallida in Hainan reduced genetic diversity, leading to a divergence in allelic frequencies at four candidate genes (CpPTR, CpMYB, CpRLPK, and CpNADK) associated with plant height. This study reveals the genetic basis of trait divergence driven by geographic dispersal and offers valuable resources for the strategic development of C. pallida breeding.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"279 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146071691","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}
Plant elicitor peptides (Peps) are a class of endogenous phytocytokine that enhances plant innate immunity against diverse pathogens. They are widely distributed in the plant kingdom, yet their interfamily compatibility of Peps perception remains controversial. In this study, two pear (Pyrus L.) Peps, PbePep4 (Pyrus betulifolia) and PdrPep6 (Pyrus ussuriensis x communis Zhongai), were identified and their function in eliciting interfamily immunity was dissected. We found that PbePep4 and PdrPep6 improved resistance of pear leaves to fire blight caused by Erwinia amylovora. Exogenous treatment with PbePep4 and PdrPep6 activated various immune responses in pear leaves, including burst of reactive oxygen species, deposition of callose, phosphorylation of Mitogen-Activated Protein Kinase, and up-regulation of defense genes. Intriguingly, these two pear peptides were able to interfamilially trigger immune responses of plants from Brassicaceae and Cucurbiaceae families. Application with PbePep4 and PdrPep6 enhanced the resistance of Brassicaceae species Arabidopsis thaliana and Brassica napus to Sclerotinia sclerotiorum, and that of Cucurbiaceae species Citrullus lanatus to Botrytis cinerea. We demonstrated that the key of these peptides to induce immunity in cross-family species is associated with the conservation of the conformed motif at the C-terminal of Pep peptides and their six active binding sites in PEPRs in cross-family species from the Rosaceae, Brassicaceae, and Cucurbiaceae. Taken together, our findings not only solved the debate whether plant Peps can only stimulate immunity within the family, but also clarified the exploitation potential of pear Peps as broad-spectrum immune inducers to control disease in crops of at least three families.
{"title":"Two pear phytocytokines PbePep4 and PdrPep6 interfamilially elicit broad-spectrum immunity against various pathogens in crops","authors":"Hai-Ting Wei, Ke Feng, Fan Xu, Xin-Zhong Cai","doi":"10.1093/hr/uhag027","DOIUrl":"https://doi.org/10.1093/hr/uhag027","url":null,"abstract":"Plant elicitor peptides (Peps) are a class of endogenous phytocytokine that enhances plant innate immunity against diverse pathogens. They are widely distributed in the plant kingdom, yet their interfamily compatibility of Peps perception remains controversial. In this study, two pear (Pyrus L.) Peps, PbePep4 (Pyrus betulifolia) and PdrPep6 (Pyrus ussuriensis x communis Zhongai), were identified and their function in eliciting interfamily immunity was dissected. We found that PbePep4 and PdrPep6 improved resistance of pear leaves to fire blight caused by Erwinia amylovora. Exogenous treatment with PbePep4 and PdrPep6 activated various immune responses in pear leaves, including burst of reactive oxygen species, deposition of callose, phosphorylation of Mitogen-Activated Protein Kinase, and up-regulation of defense genes. Intriguingly, these two pear peptides were able to interfamilially trigger immune responses of plants from Brassicaceae and Cucurbiaceae families. Application with PbePep4 and PdrPep6 enhanced the resistance of Brassicaceae species Arabidopsis thaliana and Brassica napus to Sclerotinia sclerotiorum, and that of Cucurbiaceae species Citrullus lanatus to Botrytis cinerea. We demonstrated that the key of these peptides to induce immunity in cross-family species is associated with the conservation of the conformed motif at the C-terminal of Pep peptides and their six active binding sites in PEPRs in cross-family species from the Rosaceae, Brassicaceae, and Cucurbiaceae. Taken together, our findings not only solved the debate whether plant Peps can only stimulate immunity within the family, but also clarified the exploitation potential of pear Peps as broad-spectrum immune inducers to control disease in crops of at least three families.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"60 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146071530","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}
Oregano (Origanum vulgare) is a highly valued aromatic herb for culinary, medicinal, and ornamental purposes. Its commercial value is largely from its essential oil (EO), which is rich in key bioactive terpenoids, such as carvacrol and thymol. Greek oregano (O. vulgare subsp. hirtum) subspecies is particularly prized for its high EO content. In this study, we generated a high-quality genome assembly of Greek oregano to investigate its evolutionary trajectory and the genetic basis of terpenoid biosynthesis. The assembly spans 709.74 Mb and is anchored to 15 chromosomes, with a scaffold N50 of 46.36 Mb. Comparative genomic analysis revealed a whole-genome duplication (WGD) event, estimated at ~59.93 million years ago (Mya), which likely contributed to the diversification of terpenoid biosynthesis pathways within the Lamiaceae family. Using a rapid screening approach, we identified Greek oregano mutants with higher EO content. Integrated genomic and transcriptomic analysis of a high-EO mutant highlighted the importance of α-linolenic acid metabolism/jasmonic acid (JA) biosynthesis pathways in EO production. Exogenous JA treatment led to upregulation of key EO biosynthetic genes and higher EO content. Furthermore, a JA-inducible bHLH transcription factor, OvbHLH13, was identified as a central regulator of terpenoid biosynthesis. Through Y1H, transcriptional activation, and EMSA assays, we demonstrated that OvbHLH13 directly bound to and transactivated the promoter of OvSDR1, which encodes a critical enzyme in thymol and carvacrol production. Collectively, this genomic resource provides valuable insights into the genetic and regulatory network controlling terpenoid biosynthesis and establishes a critical genomic foundation for molecular breeding of Greek oregano.
{"title":"Chromosome-level genome assembly of Origanum vulgare subsp. hirtum reveals evolutionary insights and regulatory modules in terpenoid biosynthesis","authors":"Tingchao Yin, Hefeng Guo, Yaolong Zhu, Yicheng Yang, Huanhuan Hao, Xinbao Liu, Junhao Lou, Caiyi Xie, Ya Wang, Haidong Yan, Linkai Huang, Yuzhu Li, Shuo Yan, Yingjun Chi, Bin Xu, Jing Zhang","doi":"10.1093/hr/uhag030","DOIUrl":"https://doi.org/10.1093/hr/uhag030","url":null,"abstract":"Oregano (Origanum vulgare) is a highly valued aromatic herb for culinary, medicinal, and ornamental purposes. Its commercial value is largely from its essential oil (EO), which is rich in key bioactive terpenoids, such as carvacrol and thymol. Greek oregano (O. vulgare subsp. hirtum) subspecies is particularly prized for its high EO content. In this study, we generated a high-quality genome assembly of Greek oregano to investigate its evolutionary trajectory and the genetic basis of terpenoid biosynthesis. The assembly spans 709.74 Mb and is anchored to 15 chromosomes, with a scaffold N50 of 46.36 Mb. Comparative genomic analysis revealed a whole-genome duplication (WGD) event, estimated at ~59.93 million years ago (Mya), which likely contributed to the diversification of terpenoid biosynthesis pathways within the Lamiaceae family. Using a rapid screening approach, we identified Greek oregano mutants with higher EO content. Integrated genomic and transcriptomic analysis of a high-EO mutant highlighted the importance of α-linolenic acid metabolism/jasmonic acid (JA) biosynthesis pathways in EO production. Exogenous JA treatment led to upregulation of key EO biosynthetic genes and higher EO content. Furthermore, a JA-inducible bHLH transcription factor, OvbHLH13, was identified as a central regulator of terpenoid biosynthesis. Through Y1H, transcriptional activation, and EMSA assays, we demonstrated that OvbHLH13 directly bound to and transactivated the promoter of OvSDR1, which encodes a critical enzyme in thymol and carvacrol production. Collectively, this genomic resource provides valuable insights into the genetic and regulatory network controlling terpenoid biosynthesis and establishes a critical genomic foundation for molecular breeding of Greek oregano.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"91 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146071692","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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