Ezekiel Ahn, Insuck Baek, Lalit Kandpal, Dapeng Zhang, Silvas Kirubakaran, Seunghyun Lim, Jishnu Bhatt, Moon S Kim, Sunchung Park, Lyndel W Meinhardt
High-throughput genotyping has revolutionized horticultural breeding, yet the efficient utilization of genomic data remains a bottleneck for germplasm curation and downstream selection. Translating complex genomic information into cost-effective and readily applicable tools for clonally propagated crops requires a shift from maximizing marker density to optimizing information content. Here, we reinterpret cacao (Theobroma cacao L.) genotyping as an information-allocation problem and introduce an information-theoretic framework for designing minimalist, trait-enriched SNP barcodes. Using a diverse international collection from Trinidad (ICGT) and an independent field trial in Puerto Rico (USDA-ARS Tropical Agriculture Research Station, TARS), we compress a 500+ SNP panel into a 32-marker ‘CacaoCipher’ barcode that preserves pairwise genetic distance structure at coarse resolution while retaining trait-aligned signal for pod index and related yield components. Barcode-space axes correlate with agronomic traits measured across environments in a limited overlap subset, supporting the portability of key signals beyond the training setting. We further quantify a heuristic ‘genomic bit budget,’ showing how information is allocated across unique identification, ancestry structure, and trait variation. Together, this framework converts cacao germplasm from an analog collection of names into a compact digital code and provides a general template for designing low-cost, high-information marker panels for germplasm QC and stratified screening in clonally propagated crops.
{"title":"Optimizing the genomic bit budget: an information-theoretic framework for trait-enriched genotyping and stratified screening in Theobroma cacao","authors":"Ezekiel Ahn, Insuck Baek, Lalit Kandpal, Dapeng Zhang, Silvas Kirubakaran, Seunghyun Lim, Jishnu Bhatt, Moon S Kim, Sunchung Park, Lyndel W Meinhardt","doi":"10.1093/hr/uhag106","DOIUrl":"https://doi.org/10.1093/hr/uhag106","url":null,"abstract":"High-throughput genotyping has revolutionized horticultural breeding, yet the efficient utilization of genomic data remains a bottleneck for germplasm curation and downstream selection. Translating complex genomic information into cost-effective and readily applicable tools for clonally propagated crops requires a shift from maximizing marker density to optimizing information content. Here, we reinterpret cacao (Theobroma cacao L.) genotyping as an information-allocation problem and introduce an information-theoretic framework for designing minimalist, trait-enriched SNP barcodes. Using a diverse international collection from Trinidad (ICGT) and an independent field trial in Puerto Rico (USDA-ARS Tropical Agriculture Research Station, TARS), we compress a 500+ SNP panel into a 32-marker ‘CacaoCipher’ barcode that preserves pairwise genetic distance structure at coarse resolution while retaining trait-aligned signal for pod index and related yield components. Barcode-space axes correlate with agronomic traits measured across environments in a limited overlap subset, supporting the portability of key signals beyond the training setting. We further quantify a heuristic ‘genomic bit budget,’ showing how information is allocated across unique identification, ancestry structure, and trait variation. Together, this framework converts cacao germplasm from an analog collection of names into a compact digital code and provides a general template for designing low-cost, high-information marker panels for germplasm QC and stratified screening in clonally propagated crops.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"17 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147489347","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}
Monk fruit (Siraitia grosvenorii, Cucurbitaceae) is globally renowned for its triterpenoid glycoside mogroside V, a high-intensity, non-caloric natural sweetener. However, its domestication and mogroside biosynthesis remain largely unknown. Here, we report a haplotype-resolved telomere-to-telomere (T2T) gapless genome for monk fruit, consisting of 14 chromosomes with genome sizes of 316.21 Mb (Hap1) and 316.07 Mb (Hap2). Comparative genomic analyses of the haplotypes revealed that structural variations and transposable elements have significantly contributed to genomic variation and architecture in monk fruit. Population genomic analyses based on 173 re-sequenced genomes indicated that cultivated monk fruit was mainly domesticated in situ from local wild populations in northern Guangxi of China, and that it likely experienced a mild domestication bottleneck, while exhibiting low genetic diversity. Demographic inference further revealed that the low genetic diversity is largely attributed to demographic changes driven by historical climate shifts. Selective sweeps were identified across all chromosomes of cultivated monk fruit, among which are genes exhibiting diverse putative functions and involved in various biosynthetic processes and secondary metabolism. This pattern of selective sweeps demonstrates the joint role of artificial selection and demographic changes in shaping the genomic landscape of cultivated monk fruit. Furthermore, comparative transcriptome analyses showed a pronounced temporally specific expression pattern among mogroside biosynthesis genes during fruit development and delineated additional candidate genes potentially involved in mogroside biosynthesis. This study not only provides insights into the domestication and mogroside biosynthesis of monk fruit, but also lays a valuable genomic foundation for its molecular breeding and mogroside-targeted synthetic biology.
{"title":"Haplotype-resolved T2T genome and population resequencing provide insights into the domestication and mogroside biosynthesis of Siraitia grosvenorii (Cucurbitaceae)","authors":"Yixuan Kou, Shulan Wang, Wei Xie, Li Dou, Dingguo Pan, Bowen Lai, Fuyan Mo, Panyu Yang, Dongchang Zeng, Sujuan Wei, Haimiao Wang, Zhiyong Zhang, Shaoqing Tang","doi":"10.1093/hr/uhag103","DOIUrl":"https://doi.org/10.1093/hr/uhag103","url":null,"abstract":"Monk fruit (Siraitia grosvenorii, Cucurbitaceae) is globally renowned for its triterpenoid glycoside mogroside V, a high-intensity, non-caloric natural sweetener. However, its domestication and mogroside biosynthesis remain largely unknown. Here, we report a haplotype-resolved telomere-to-telomere (T2T) gapless genome for monk fruit, consisting of 14 chromosomes with genome sizes of 316.21 Mb (Hap1) and 316.07 Mb (Hap2). Comparative genomic analyses of the haplotypes revealed that structural variations and transposable elements have significantly contributed to genomic variation and architecture in monk fruit. Population genomic analyses based on 173 re-sequenced genomes indicated that cultivated monk fruit was mainly domesticated in situ from local wild populations in northern Guangxi of China, and that it likely experienced a mild domestication bottleneck, while exhibiting low genetic diversity. Demographic inference further revealed that the low genetic diversity is largely attributed to demographic changes driven by historical climate shifts. Selective sweeps were identified across all chromosomes of cultivated monk fruit, among which are genes exhibiting diverse putative functions and involved in various biosynthetic processes and secondary metabolism. This pattern of selective sweeps demonstrates the joint role of artificial selection and demographic changes in shaping the genomic landscape of cultivated monk fruit. Furthermore, comparative transcriptome analyses showed a pronounced temporally specific expression pattern among mogroside biosynthesis genes during fruit development and delineated additional candidate genes potentially involved in mogroside biosynthesis. This study not only provides insights into the domestication and mogroside biosynthesis of monk fruit, but also lays a valuable genomic foundation for its molecular breeding and mogroside-targeted synthetic biology.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"59 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147489348","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}
Accurately predicting the performance of trees and crops across diverse and changing climates is essential for matching genotypes to both current and future environments. Yet modelling the complex interplay among genotype, environment, and phenotype in multi-environment trials remains a major challenge. Here, we introduce a unified framework, polygenic environmental interaction (PEI), directly models genotype-by-environment interactions through integrating genotypes and environmental covariates. We implemented an ensemble of 15 estimators spanning parametric, non-parametric, and machine-learning approaches. We then benchmarked our framework against the classical reaction norm (RN) using three genetically distinct populations and three traits with variable genetic architectures. Furthermore, we released an open-source R package, Multiple-Environments Genomic Selection (MMGS), on GitHub. Together, our study offers a flexible and computationally efficient approach for multi-environment genomic prediction, enhancing breeding efficiency, providing deeper insights into modelling the genotype-environment-phenotype continuum.
{"title":"MMGS: A novel genomic prediction framework to integrate genotype, environment and their interactions for multi-environment breeding trials","authors":"Mingjia Zhu, Zeyu Zheng, Wei Liu, Yu Han, Wenjie Mou, Tongming Yin, Xiaogang Dai, Huaitong Wu, Yongzhi Yang, Yanjun Zan, Jianquan Liu","doi":"10.1093/hr/uhag035","DOIUrl":"https://doi.org/10.1093/hr/uhag035","url":null,"abstract":"Accurately predicting the performance of trees and crops across diverse and changing climates is essential for matching genotypes to both current and future environments. Yet modelling the complex interplay among genotype, environment, and phenotype in multi-environment trials remains a major challenge. Here, we introduce a unified framework, polygenic environmental interaction (PEI), directly models genotype-by-environment interactions through integrating genotypes and environmental covariates. We implemented an ensemble of 15 estimators spanning parametric, non-parametric, and machine-learning approaches. We then benchmarked our framework against the classical reaction norm (RN) using three genetically distinct populations and three traits with variable genetic architectures. Furthermore, we released an open-source R package, Multiple-Environments Genomic Selection (MMGS), on GitHub. Together, our study offers a flexible and computationally efficient approach for multi-environment genomic prediction, enhancing breeding efficiency, providing deeper insights into modelling the genotype-environment-phenotype continuum.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"60 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147462166","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}
Lushan Ghimire, Yichun Wang, Paul Adunola, Wardatou Boukari, Gonzalo Casorzo, Felix Enciso-Rodriguez, Philip F Harmon, Juliana Benevenuto, Patricio R Munoz
Botrytis cinerea is a broad host range fungal pathogen causing gray mold disease and crop losses worldwide. In blueberries, symptoms include blossom blight in the field and postharvest fruit rot, affecting the entire supply chain. With control options constrained by regulatory restrictions and fungicide resistance, the dissection of the genetic and molecular basis of blueberry response to B. cinerea can accelerate breeding for resistance. In this study, we phenotyped 354 blueberry selections using a high-throughput Botrytis infection fruit assay. The same population was genotyped by targeted sequencing for genome-wide association study (GWAS). In addition, we performed RNA-seq time-course (0–96 hpi) for resistant and susceptible genotypes. Our results showed a continuum of tolerance levels and moderate narrow-sense heritability estimates for the disease-related traits (0.46–0.61). GWAS identified small-effect loci, consistent with quantitative resistance observed in other host plant species. Intersecting differentially expressed genes with GWAS intervals revealed eight candidate genes. Transcriptomic analyses showed that, at early stages, the resistant genotype upregulated components of basal innate immunity, including wax and cutin biosynthesis, responses to wounding and fungal-derived molecules, the MAPK cascade, and ethylene and jasmonate signaling. In contrast, susceptible genotypes displayed delayed activation of these defense pathways and altered cell wall–related processes. The moderate correlation between disease traits and wax bloom further supported a role for wax in disease response. Together, our findings provide molecular markers and candidate genes for Botrytis fruit rot resistance in blueberry with significant applications in breeding programs and opportunities to future validation studies.
{"title":"Integrative GWAS and transcriptomic analyses reveal markers and candidate genes associated with resistance to Botrytis cinerea fruit rot in blueberry","authors":"Lushan Ghimire, Yichun Wang, Paul Adunola, Wardatou Boukari, Gonzalo Casorzo, Felix Enciso-Rodriguez, Philip F Harmon, Juliana Benevenuto, Patricio R Munoz","doi":"10.1093/hr/uhag092","DOIUrl":"https://doi.org/10.1093/hr/uhag092","url":null,"abstract":"Botrytis cinerea is a broad host range fungal pathogen causing gray mold disease and crop losses worldwide. In blueberries, symptoms include blossom blight in the field and postharvest fruit rot, affecting the entire supply chain. With control options constrained by regulatory restrictions and fungicide resistance, the dissection of the genetic and molecular basis of blueberry response to B. cinerea can accelerate breeding for resistance. In this study, we phenotyped 354 blueberry selections using a high-throughput Botrytis infection fruit assay. The same population was genotyped by targeted sequencing for genome-wide association study (GWAS). In addition, we performed RNA-seq time-course (0–96 hpi) for resistant and susceptible genotypes. Our results showed a continuum of tolerance levels and moderate narrow-sense heritability estimates for the disease-related traits (0.46–0.61). GWAS identified small-effect loci, consistent with quantitative resistance observed in other host plant species. Intersecting differentially expressed genes with GWAS intervals revealed eight candidate genes. Transcriptomic analyses showed that, at early stages, the resistant genotype upregulated components of basal innate immunity, including wax and cutin biosynthesis, responses to wounding and fungal-derived molecules, the MAPK cascade, and ethylene and jasmonate signaling. In contrast, susceptible genotypes displayed delayed activation of these defense pathways and altered cell wall–related processes. The moderate correlation between disease traits and wax bloom further supported a role for wax in disease response. Together, our findings provide molecular markers and candidate genes for Botrytis fruit rot resistance in blueberry with significant applications in breeding programs and opportunities to future validation studies.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"10 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147447633","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}
Loquat (Eriobotrya japonica Lindl.), a subtropical evergreen species of the Rosaceae family, faces industry constraints in industrial development due to its sensitivity to freezing temperatures and low photosynthetic efficiency. Polyploid loquats, particularly triploids, exhibit enhanced stress resistance, vigorous growth, and seedless fruit production. in this study, triploid F1 progeny (B431 × GZ23) were obtained through hybridization between diploid (GZ23) and tetraploid (B431) parents. Under − 3°C stress, the triploid lines exhibited significantly improved freezing tolerance and photosynthetic performance, as evidenced by chlorophyll fluorescence parameters and ultrastructural integrity. Lipidomics profiling across all B431 × GZ23 lines revealed that phosphatidylcholine (PC), particularly the abundant unsaturated PC species 18:2/18:2, played a key role in these adaptive advantages. Compared to the parental lines, EjFAD2 expression was specifically upregulated in triploid loquats under freezing stress. Consistent lipidomic and gene expression patterns across three B431 × GZ23 lines ruled out line-specific mutations. Heterologous expression of EjFAD2 in Arabidopsis increased freezing tolerance. Co-expression analysis identified EjMYBS3 as a regulator that binds to the EjFAD2 promoter, and its overexpression in transgenic Arabidopsis enhanced freezing tolerance. Transient expression of EjFAD2 and EjMYBS3 increased the content of PC 18:2/18:2 in loquat, which contributed to the maintenance of photosystem activity under freezing stress, thereby enhancing the freezing tolerance of loquat. Collectively, these findings provide preliminary insights into the molecular mechanisms underlying cold resistance in polyploid loquats and highlight the regulatory role of EjFAD2 and EjMYBS3 in freezing stress response.
{"title":"Triploid loquat maintains photosynthetic stability under freezing stress through excessive accumulation of unsaturated lipids","authors":"Mingxiu Liu, Xiaodong Suo, Xun Xu, Hao Yang, Mubasshir Hussain, Danlong Jing, Jiangbo Dang, Di Wu, Shuming Wang, Yan Xia, Qiao He, Guolu Liang, Qigao Guo","doi":"10.1093/hr/uhag096","DOIUrl":"https://doi.org/10.1093/hr/uhag096","url":null,"abstract":"Loquat (Eriobotrya japonica Lindl.), a subtropical evergreen species of the Rosaceae family, faces industry constraints in industrial development due to its sensitivity to freezing temperatures and low photosynthetic efficiency. Polyploid loquats, particularly triploids, exhibit enhanced stress resistance, vigorous growth, and seedless fruit production. in this study, triploid F1 progeny (B431 × GZ23) were obtained through hybridization between diploid (GZ23) and tetraploid (B431) parents. Under − 3°C stress, the triploid lines exhibited significantly improved freezing tolerance and photosynthetic performance, as evidenced by chlorophyll fluorescence parameters and ultrastructural integrity. Lipidomics profiling across all B431 × GZ23 lines revealed that phosphatidylcholine (PC), particularly the abundant unsaturated PC species 18:2/18:2, played a key role in these adaptive advantages. Compared to the parental lines, EjFAD2 expression was specifically upregulated in triploid loquats under freezing stress. Consistent lipidomic and gene expression patterns across three B431 × GZ23 lines ruled out line-specific mutations. Heterologous expression of EjFAD2 in Arabidopsis increased freezing tolerance. Co-expression analysis identified EjMYBS3 as a regulator that binds to the EjFAD2 promoter, and its overexpression in transgenic Arabidopsis enhanced freezing tolerance. Transient expression of EjFAD2 and EjMYBS3 increased the content of PC 18:2/18:2 in loquat, which contributed to the maintenance of photosystem activity under freezing stress, thereby enhancing the freezing tolerance of loquat. Collectively, these findings provide preliminary insights into the molecular mechanisms underlying cold resistance in polyploid loquats and highlight the regulatory role of EjFAD2 and EjMYBS3 in freezing stress response.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"90 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147461962","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 grafting is a horticultural technique used to join different plants with desirable traits. However, graft incompatibility limits its application, especially in agriculturally important Fabaceae species. To enhance grafting efficiency, we conducted chemical screening utilizing an in vitro grafting (IVG) system in Fabaceae. In this study, we screened 3000 artificial chemical compounds and identified a compound, designated graft-promoting molecule 1 (GPM1), which enhanced graft adhesion in Fabaceae species—including Phaseolus coccineus, Vigna unguiculata, Vigna angularis, and Glycine max—as well as in V. unguiculata/G. max hetero-IVGs at 5 days after grafting (DAG). Notably, GPM1 also increased adhesive force in Nicotiana benthamiana IVGs and improved survival rates in Arabidopsis thaliana micrografting, indicating that its activity is not restricted to Fabaceae. Transcriptome analysis of P. coccineus IVGs at 1 DAG revealed that application of GPM1 induced the upregulation of cell wall modification genes, including PvEXPA5, PvEXPA22, and PvEXPA25. In contrast, treatment with 2,4-dichlorophenoxyacetic acid (2,4-D) induced a broader transcriptional response, predominantly upregulating genes related to cell division. In G. max stem grafting, GPM1 enhanced scion growth and promoted the formation of larger callus cells at the graft junction. Moreover, qRT-PCR analysis revealed that GPM1 significantly upregulated Glyma.07G229000, a homolog of PvEXPA5. The upregulation of cell wall-associated genes by GPM1 is consistent with a role in early graft union formation, potentially by facilitating tissue adhesion at the graft interface. Collectively, this study identifies GPM1 as a chemical regulator that enhances graft adhesion and provides insight into molecular processes associated with early graft adhesion.
{"title":"Chemical Screening in Fabaceae Identified GPM1 as a Novel Compound Enhancing Early Graft Adhesion","authors":"Qianqian Luo, Xueyao Shu, Ayato Sato, Yaichi Kawakatsu, Kentaro Okada, Frank Opoku-Agyemang, Ken-ichi Kurotani, Michitaka Notaguchi","doi":"10.1093/hr/uhag095","DOIUrl":"https://doi.org/10.1093/hr/uhag095","url":null,"abstract":"Plant grafting is a horticultural technique used to join different plants with desirable traits. However, graft incompatibility limits its application, especially in agriculturally important Fabaceae species. To enhance grafting efficiency, we conducted chemical screening utilizing an in vitro grafting (IVG) system in Fabaceae. In this study, we screened 3000 artificial chemical compounds and identified a compound, designated graft-promoting molecule 1 (GPM1), which enhanced graft adhesion in Fabaceae species—including Phaseolus coccineus, Vigna unguiculata, Vigna angularis, and Glycine max—as well as in V. unguiculata/G. max hetero-IVGs at 5 days after grafting (DAG). Notably, GPM1 also increased adhesive force in Nicotiana benthamiana IVGs and improved survival rates in Arabidopsis thaliana micrografting, indicating that its activity is not restricted to Fabaceae. Transcriptome analysis of P. coccineus IVGs at 1 DAG revealed that application of GPM1 induced the upregulation of cell wall modification genes, including PvEXPA5, PvEXPA22, and PvEXPA25. In contrast, treatment with 2,4-dichlorophenoxyacetic acid (2,4-D) induced a broader transcriptional response, predominantly upregulating genes related to cell division. In G. max stem grafting, GPM1 enhanced scion growth and promoted the formation of larger callus cells at the graft junction. Moreover, qRT-PCR analysis revealed that GPM1 significantly upregulated Glyma.07G229000, a homolog of PvEXPA5. The upregulation of cell wall-associated genes by GPM1 is consistent with a role in early graft union formation, potentially by facilitating tissue adhesion at the graft interface. Collectively, this study identifies GPM1 as a chemical regulator that enhances graft adhesion and provides insight into molecular processes associated with early graft adhesion.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"24 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147447631","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}
Isabel Padilla-Roji, Alejandro Jiménez-Sánchez, Sara Yugueros, Hugo Mélida, Álvaro Polonio, Dolores Fernández Ortuño, Alejandro Pérez-García
Cucurbit powdery mildew, predominantly caused by Podosphaera xanthii, poses a major threat to global cucurbit production due to the pathogen’s rapid adaptability and resistance to conventional fungicides. This growing challenge highlights the urgent need for alternative, sustainable disease management strategies. As the primary interface between the fungus, host plant, and environment, the fungal cell wall emerges as a strategic target for development of innovative control approaches. This study focuses on ECM33, a glycophosphatidylinositol (GPI)-anchored protein believed to play a role in cell wall architecture and integrity, although its specific biochemical function remains undefined. In silico structural modeling revealed that PxECM33 resembles leucine-rich repeat proteins and contains potential carbohydrate-binding motifs. Recombinant PxECM33 exhibited binding affinity for chitin, β-glucans, and mannans, the main glycosidic components of the P. xanthii cell wall, supporting these structural predictions. Molecular docking analyses uncovered distinct ligand-specific interactions with these carbohydrates, further implicating PxECM33 in cell wall dynamics. Silencing PxECM33 via RNA interference significantly impaired fungal growth and caused pronounced cell wall disorganization. Notably, dual silencing with the melon immune receptor gene CmCERK1 mitigated these defects, suggesting that PxECM33 may function in masking immunogenic oligosaccharides to evade host detection. Furthermore, spray-induced gene silencing (SIGS) targeting PxECM33 effectively reduced disease symptoms in melon plants, highlighting its potential as a sustainable and non-toxic biocontrol strategy. Given the high sequence conservation of ECM33 among ascomycete fungi, these findings support its candidacy as a broad-spectrum molecular target for managing powdery mildew in cucurbits and potentially other crops.
{"title":"Cracking the wall: The fungal cell wall assembly protein ECM33 is a promising molecular target in powdery mildew fungi","authors":"Isabel Padilla-Roji, Alejandro Jiménez-Sánchez, Sara Yugueros, Hugo Mélida, Álvaro Polonio, Dolores Fernández Ortuño, Alejandro Pérez-García","doi":"10.1093/hr/uhag101","DOIUrl":"https://doi.org/10.1093/hr/uhag101","url":null,"abstract":"Cucurbit powdery mildew, predominantly caused by Podosphaera xanthii, poses a major threat to global cucurbit production due to the pathogen’s rapid adaptability and resistance to conventional fungicides. This growing challenge highlights the urgent need for alternative, sustainable disease management strategies. As the primary interface between the fungus, host plant, and environment, the fungal cell wall emerges as a strategic target for development of innovative control approaches. This study focuses on ECM33, a glycophosphatidylinositol (GPI)-anchored protein believed to play a role in cell wall architecture and integrity, although its specific biochemical function remains undefined. In silico structural modeling revealed that PxECM33 resembles leucine-rich repeat proteins and contains potential carbohydrate-binding motifs. Recombinant PxECM33 exhibited binding affinity for chitin, β-glucans, and mannans, the main glycosidic components of the P. xanthii cell wall, supporting these structural predictions. Molecular docking analyses uncovered distinct ligand-specific interactions with these carbohydrates, further implicating PxECM33 in cell wall dynamics. Silencing PxECM33 via RNA interference significantly impaired fungal growth and caused pronounced cell wall disorganization. Notably, dual silencing with the melon immune receptor gene CmCERK1 mitigated these defects, suggesting that PxECM33 may function in masking immunogenic oligosaccharides to evade host detection. Furthermore, spray-induced gene silencing (SIGS) targeting PxECM33 effectively reduced disease symptoms in melon plants, highlighting its potential as a sustainable and non-toxic biocontrol strategy. Given the high sequence conservation of ECM33 among ascomycete fungi, these findings support its candidacy as a broad-spectrum molecular target for managing powdery mildew in cucurbits and potentially other crops.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"16 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147447635","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}
Pan Shu, Qinlu Zheng, Ziling You, Yun Zhu, Xi Cheng, Yuan Qing, Xin Yao, Jing Li, Lin Shen
Fruits and vegetables are key components of the human diet, valued for their unique textures and flavors. In recent years, numerous studies have demonstrated that individual transcription factors (TFs) can simultaneously regulate two biological processes; these TFs are defined as bifunctional TFs. However, systematic reviews on these bifunctional TFs in fruits and vegetables remain limited. This review systematically summarizes current knowledge on bifunctional TFs in fruits and vegetables, focusing on three themes: (i) molecular mechanisms (cis-element diversity, partner switching, post-translational); (ii) network topology (hubs versus bottlenecks); and (iii) agronomic trade-offs. Meanwhile, the functional conservation and divergence of homologous TFs in different fruits and vegetables have also been investigated. In addition, we elaborate how key TF families, including MYB, bHLH, WRKY, ERF, and NAC, regulate diverse physiological processes in fruits and vegetables via dual mechanisms. We also identify several limitations in the existing literature, such as insufficient understanding of bifunctional regulatory mechanisms, incomplete identification of target genes, and inadequate exploration of crop applications.
{"title":"Bifunctional Transcription Factors:Recent Advances in Growth and Development, Stress Resistance, and Quality Formation of Fruits and Vegetables","authors":"Pan Shu, Qinlu Zheng, Ziling You, Yun Zhu, Xi Cheng, Yuan Qing, Xin Yao, Jing Li, Lin Shen","doi":"10.1093/hr/uhag100","DOIUrl":"https://doi.org/10.1093/hr/uhag100","url":null,"abstract":"Fruits and vegetables are key components of the human diet, valued for their unique textures and flavors. In recent years, numerous studies have demonstrated that individual transcription factors (TFs) can simultaneously regulate two biological processes; these TFs are defined as bifunctional TFs. However, systematic reviews on these bifunctional TFs in fruits and vegetables remain limited. This review systematically summarizes current knowledge on bifunctional TFs in fruits and vegetables, focusing on three themes: (i) molecular mechanisms (cis-element diversity, partner switching, post-translational); (ii) network topology (hubs versus bottlenecks); and (iii) agronomic trade-offs. Meanwhile, the functional conservation and divergence of homologous TFs in different fruits and vegetables have also been investigated. In addition, we elaborate how key TF families, including MYB, bHLH, WRKY, ERF, and NAC, regulate diverse physiological processes in fruits and vegetables via dual mechanisms. We also identify several limitations in the existing literature, such as insufficient understanding of bifunctional regulatory mechanisms, incomplete identification of target genes, and inadequate exploration of crop applications.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"9 11 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147447642","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}
Zhang Renhong, Wang Shuo, Liu Jiangang, Jian Yinqiao, Qin Junhong, Jin Liping, He Ming, Xu Jianfei
Potato (Solanum tuberosum L.) is a globally important tuber crop and a vital component of the food system. Tuber skin texture is a key quality trait that influences market appearance and is closely associated with resistance to biotic and abiotic stresses as well as tolerance to mechanical damage. However, the genetic basis and regulatory mechanisms underlying this trait remain poorly understood. In this study, we investigated the genetic and molecular mechanisms underlying potato tuber skin texture. A quantitative trait locus (QTL) for tuber skin texture was mapped to a 1.94 Mb interval on chromosome 4 using bulked segregant analysis of a segregating population derived from a cross between russet-skinned variety Innovator and smooth-skinned variety Zhongshuzao43 (Z43). The tuber skin of Innovator contained more cell layers than Z43 and developed progressive cracking during tuber expansion. Innovator also exhibited lower suberin content but higher lignin accumulation in tuber skin compared to Z43. Transcriptome profiling across multiple developmental stages identified a distinct gene expression cluster enriched in pathways related to lignin and suberin biosynthesis. Integrating genes within the QTL with this expression cluster revealed StPXG4, which encodes a peroxygenase, as strongly correlated with skin texture. StPXG4 showed significantly higher expression in commercial smooth-skinned varieties than in russet-skinned varieties. Co-expression analysis further identified two potential upstream regulators of StPXG4, namely StMYB103 and StMYB58. These findings provide key insights into the genetic regulation of tuber skin texture and identify candidate genes that could be targeted to improve tuber appearance and stress tolerance through molecular breeding.
{"title":"Genetic architecture and major genes for tuber skin texture in potato","authors":"Zhang Renhong, Wang Shuo, Liu Jiangang, Jian Yinqiao, Qin Junhong, Jin Liping, He Ming, Xu Jianfei","doi":"10.1093/hr/uhag102","DOIUrl":"https://doi.org/10.1093/hr/uhag102","url":null,"abstract":"Potato (Solanum tuberosum L.) is a globally important tuber crop and a vital component of the food system. Tuber skin texture is a key quality trait that influences market appearance and is closely associated with resistance to biotic and abiotic stresses as well as tolerance to mechanical damage. However, the genetic basis and regulatory mechanisms underlying this trait remain poorly understood. In this study, we investigated the genetic and molecular mechanisms underlying potato tuber skin texture. A quantitative trait locus (QTL) for tuber skin texture was mapped to a 1.94 Mb interval on chromosome 4 using bulked segregant analysis of a segregating population derived from a cross between russet-skinned variety Innovator and smooth-skinned variety Zhongshuzao43 (Z43). The tuber skin of Innovator contained more cell layers than Z43 and developed progressive cracking during tuber expansion. Innovator also exhibited lower suberin content but higher lignin accumulation in tuber skin compared to Z43. Transcriptome profiling across multiple developmental stages identified a distinct gene expression cluster enriched in pathways related to lignin and suberin biosynthesis. Integrating genes within the QTL with this expression cluster revealed StPXG4, which encodes a peroxygenase, as strongly correlated with skin texture. StPXG4 showed significantly higher expression in commercial smooth-skinned varieties than in russet-skinned varieties. Co-expression analysis further identified two potential upstream regulators of StPXG4, namely StMYB103 and StMYB58. These findings provide key insights into the genetic regulation of tuber skin texture and identify candidate genes that could be targeted to improve tuber appearance and stress tolerance through molecular breeding.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"127 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147447644","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}
Chitooligosaccharides, such as chitin, are essential components of fungal cell walls and have thus naturally been selected as microbe-associated molecular patterns detected by plants to initiate defense mechanisms. These molecules are typically recognized by the lysin motif receptor-like kinases (LysM RLKs) at the plasma membrane. While chitin perception is well elucidated in Arabidopsis thaliana and other plant species, the recognition mechanisms of its deacetylated form, chitosan, remain poorly investigated despite its use as a biocontrol strategy to protect crops against pathogens. Here, we investigated the role of the two grapevine orthologs of AtLYK4, which participate in the tripartite complex for chitin perception in A. thaliana. Using a dual approach consisting of the functional complementation of the atlyk4/5 double mutant and CRISPR-Cas9 genome editing in Vitis vinifera, we showed that VvLYK4–2 is involved in both chitosan- and chitin-induced immune responses, encompassing MAPK phosphorylation and defense gene expression. Furthermore, grapevine in vitro plantlets lacking VvLYK4–2 exhibited a significantly reduced response to chitosan while retaining a low-intensity response to chitin, potentially due to the presence of VvLYK5–1. Finally, VvLYK4–2 produced in a heterologous system showed binding to chitosan oligomers and, to a lesser extent, to chitin oligomers. These findings indicate that this pattern recognition receptor plays a crucial role in the perception of chitosan oligomers and has thus potential for selective breeding purposes. This discovery may also help to better understand the partial lack of efficacy of chitosan-based plant defense stimulants used in viticulture.
{"title":"The grapevine LysM receptor kinase VvLYK4–2 is a key player in chitosan-triggered immune responses.","authors":"Thibault Roudaire, Jérémy Villette, Tania Marzari, Daphnée Brulé, Stéphanie Pradeau, Sébastien Fort, David Landry, Benoit Lefebvre, Marie-Claire Héloir, Benoit Poinssot","doi":"10.1093/hr/uhag097","DOIUrl":"https://doi.org/10.1093/hr/uhag097","url":null,"abstract":"Chitooligosaccharides, such as chitin, are essential components of fungal cell walls and have thus naturally been selected as microbe-associated molecular patterns detected by plants to initiate defense mechanisms. These molecules are typically recognized by the lysin motif receptor-like kinases (LysM RLKs) at the plasma membrane. While chitin perception is well elucidated in Arabidopsis thaliana and other plant species, the recognition mechanisms of its deacetylated form, chitosan, remain poorly investigated despite its use as a biocontrol strategy to protect crops against pathogens. Here, we investigated the role of the two grapevine orthologs of AtLYK4, which participate in the tripartite complex for chitin perception in A. thaliana. Using a dual approach consisting of the functional complementation of the atlyk4/5 double mutant and CRISPR-Cas9 genome editing in Vitis vinifera, we showed that VvLYK4–2 is involved in both chitosan- and chitin-induced immune responses, encompassing MAPK phosphorylation and defense gene expression. Furthermore, grapevine in vitro plantlets lacking VvLYK4–2 exhibited a significantly reduced response to chitosan while retaining a low-intensity response to chitin, potentially due to the presence of VvLYK5–1. Finally, VvLYK4–2 produced in a heterologous system showed binding to chitosan oligomers and, to a lesser extent, to chitin oligomers. These findings indicate that this pattern recognition receptor plays a crucial role in the perception of chitosan oligomers and has thus potential for selective breeding purposes. This discovery may also help to better understand the partial lack of efficacy of chitosan-based plant defense stimulants used in viticulture.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"19 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147447643","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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