Understanding the genetic and regulatory mechanisms underlying wood traits and secondary cell wall (SCW) development in Ginkgo biloba is crucial for improving wood quality. We identified key genes related to wood traits and SCW development through integrated genome-wide association studies (GWAS), transcriptome-wide association studies (TWAS), and weighted gene co-expression network analysis (WGCNA). Cellulose biosynthesis in the SCW is catalyzed by the CesA4–CesA7–CesA8 complex encoded by GbCesA4, GbCesA7, and GbCesA8A/8B. These CesA genes form a co-expression network with TUBA/TUBB and EG, indicating coordination among cellulose synthesis, cytoskeletal guidance, and cell wall remodeling. Additionally, loss of function of GbCesA8B caused only a slight reduction in cellulose content, supporting potential functional redundancy between GbCesA8A and GbCesA8B. For hemicellulose biosynthesis, GbCSLA9A/9B and IRX9/IRX14 were major contributors to mannan/glucomannan and xylan synthesis, respectively, and formed a co-expression network with UXS, UXE, IRX7, GXMT, and URGT, spanning nucleotide sugar supply, transport, and polymer elongation and modification. Moreover, MYB46 may regulate mannan/glucomannan biosynthesis in the SCW by activating CSLA9 transcription. For lignin biosynthesis, TWAS identified multiple genes involved in phenylalanine biosynthesis, phenylpropanoid metabolism, and lignin monomer polymerization, including ADT/PDT, PAL, and PER, as well as MYB91 and several bHLH genes that may positively regulate lignin accumulation. Furthermore, several transcription factors potentially involved in SCW development were identified, including GATA9 as a putative positive regulator, WRKY12 and HB15 as potential negative regulators, and ELF6, which may facilitate tracheid expansion. Our findings provide valuable insights into the genetic regulation of wood traits and SCW development in Ginkgo.
{"title":"Revealing the genetic regulation of wood traits and secondary cell wall development in Ginkgo biloba : an integrated analysis from the perspectives of GWAS, TWAS, and WGCNA","authors":"Tianhui Gao, Jiazhou Shang, Xiongjie Li, Yidong Chen, Jing Guo, Fangfang Fu, Fuliang Cao, Guibin Wang","doi":"10.1093/hr/uhag062","DOIUrl":"https://doi.org/10.1093/hr/uhag062","url":null,"abstract":"Understanding the genetic and regulatory mechanisms underlying wood traits and secondary cell wall (SCW) development in Ginkgo biloba is crucial for improving wood quality. We identified key genes related to wood traits and SCW development through integrated genome-wide association studies (GWAS), transcriptome-wide association studies (TWAS), and weighted gene co-expression network analysis (WGCNA). Cellulose biosynthesis in the SCW is catalyzed by the CesA4–CesA7–CesA8 complex encoded by GbCesA4, GbCesA7, and GbCesA8A/8B. These CesA genes form a co-expression network with TUBA/TUBB and EG, indicating coordination among cellulose synthesis, cytoskeletal guidance, and cell wall remodeling. Additionally, loss of function of GbCesA8B caused only a slight reduction in cellulose content, supporting potential functional redundancy between GbCesA8A and GbCesA8B. For hemicellulose biosynthesis, GbCSLA9A/9B and IRX9/IRX14 were major contributors to mannan/glucomannan and xylan synthesis, respectively, and formed a co-expression network with UXS, UXE, IRX7, GXMT, and URGT, spanning nucleotide sugar supply, transport, and polymer elongation and modification. Moreover, MYB46 may regulate mannan/glucomannan biosynthesis in the SCW by activating CSLA9 transcription. For lignin biosynthesis, TWAS identified multiple genes involved in phenylalanine biosynthesis, phenylpropanoid metabolism, and lignin monomer polymerization, including ADT/PDT, PAL, and PER, as well as MYB91 and several bHLH genes that may positively regulate lignin accumulation. Furthermore, several transcription factors potentially involved in SCW development were identified, including GATA9 as a putative positive regulator, WRKY12 and HB15 as potential negative regulators, and ELF6, which may facilitate tracheid expansion. Our findings provide valuable insights into the genetic regulation of wood traits and SCW development in Ginkgo.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"54 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147292726","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}
Yu-Si Yang, Yu-Ke Du, Jia-Li Li, Yong-Kang Wang, Cun-Yu Li, Xin-Qiang Zheng, Jian-Hui Ye, Yue-Rong Liang, Zhou-Tao Fang, Jian-Liang Lu
Dihydrochalcones (DHCs) are highly accumulated in tender leaves of Lithocarpus litseifolius, but their biosynthetic pathway and accumulation mechanism remain unclear. In this study, candidate genes including one cinnamoyl-CoA reductase (LlCCR), two double bond reductases (LlDBR1~2), three aldehyde hydrogenases (LlALDH1~3), two 4-coumaroyl: CoA ligases (Ll4CL1~2) and four phloretin glycosyltransferases (LlP4′GT, LlP2′GT1~3) were comprehensively investigated. The substrate specificities and catalytic kinetics of these genes-encoded enzymes were achieved. Through successive catalysis of LlALDH1, Ll4CL2 and chalcone synthase 1 (LlCHS1) or combined action of LlCCR and LlCHS1, phloretin was biosynthesized from direct precursor dihydro-p-coumaraldehyde which had been converted from initial precursor p-coumaroyl-CoA by LlCCR-mediated carboxylic acid reduction and LlDBR1-catalyzed α,β-double bond saturation. High accumulation of the DHCs in tender leaves of L. litseifolius was mainly driven by efficient catalysis of LlCCR towards p-coumaroyl-CoA and highly expressed genes in the pathway, especially the LlP4′GT and LlP2′GT1 which contributed to biosynthesis of trilobatin and phlorizin, respectively. Antisense oligodeoxyribonucleotide treatments against the LlCCR, LlDBR1, LlALDH1, Ll4CL2, LlP4′GT and LlP2′GT1 significantly reduced transcripts of the target genes and content of DHCs, confirming these genes might be involved in the pathway. This finding provides insight into the biosynthesis and accumulation mechanism of DHCs in planta.
{"title":"Study on biosynthesis pathway and accumulation mechanism of the dihydrochalcones in Lithocarpus litseifolius","authors":"Yu-Si Yang, Yu-Ke Du, Jia-Li Li, Yong-Kang Wang, Cun-Yu Li, Xin-Qiang Zheng, Jian-Hui Ye, Yue-Rong Liang, Zhou-Tao Fang, Jian-Liang Lu","doi":"10.1093/hr/uhag061","DOIUrl":"https://doi.org/10.1093/hr/uhag061","url":null,"abstract":"Dihydrochalcones (DHCs) are highly accumulated in tender leaves of Lithocarpus litseifolius, but their biosynthetic pathway and accumulation mechanism remain unclear. In this study, candidate genes including one cinnamoyl-CoA reductase (LlCCR), two double bond reductases (LlDBR1~2), three aldehyde hydrogenases (LlALDH1~3), two 4-coumaroyl: CoA ligases (Ll4CL1~2) and four phloretin glycosyltransferases (LlP4′GT, LlP2′GT1~3) were comprehensively investigated. The substrate specificities and catalytic kinetics of these genes-encoded enzymes were achieved. Through successive catalysis of LlALDH1, Ll4CL2 and chalcone synthase 1 (LlCHS1) or combined action of LlCCR and LlCHS1, phloretin was biosynthesized from direct precursor dihydro-p-coumaraldehyde which had been converted from initial precursor p-coumaroyl-CoA by LlCCR-mediated carboxylic acid reduction and LlDBR1-catalyzed α,β-double bond saturation. High accumulation of the DHCs in tender leaves of L. litseifolius was mainly driven by efficient catalysis of LlCCR towards p-coumaroyl-CoA and highly expressed genes in the pathway, especially the LlP4′GT and LlP2′GT1 which contributed to biosynthesis of trilobatin and phlorizin, respectively. Antisense oligodeoxyribonucleotide treatments against the LlCCR, LlDBR1, LlALDH1, Ll4CL2, LlP4′GT and LlP2′GT1 significantly reduced transcripts of the target genes and content of DHCs, confirming these genes might be involved in the pathway. This finding provides insight into the biosynthesis and accumulation mechanism of DHCs in planta.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"25 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147292757","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}
Salvia miltiorrhiza, a medicinal plant of high value, faces significant yield and quality losses due to salt stress. Identifying salt tolerance genes is therefore essential for breeding resilient varieties. Gibberellin (GA) metabolism and signaling are modulated by diverse factors, with GA 2-oxidase (GA2ox) playing a key role in stress adaptation by inactivating GA and fine-tuning growth under adverse conditions. In this work, we identified 12 GA2ox genes in S. miltiorrhiza and generated a SmGA2ox4 transgenic line. Heterologous expression in Arabidopsis thaliana improved salt tolerance through enhanced germination, root growth, antioxidant activity, and stress-related physiological markers. Similar results were observed in transgenic hairy roots of S. miltiorrhiza. HPLC analysis further showed that SmGA2ox4 overexpression promoted tanshinone accumulation but suppressed salvianolic acid biosynthesis, whereas RNAi-mediated silencing had the opposite effect. Thus, SmGA2ox4 acts as a dual-function regulator, enhancing both salt tolerance and tanshinone production. This study establishes a novel link between GA2ox-mediated stress response and secondary metabolism in S. miltiorrhiza, providing a basis for engineering stress-resistant, high-quality varieties.
{"title":"SmGA2ox4 Plays a Positive Role in Improving the Salt Tolerance and Tanshinone Accumulation of Salvia miltiorrhiza","authors":"Sijia Zeng, Yifan Li, Shiying Wang, Yihua Liang, Zhijing Yu, Zisong Yang, Pengda Ma, Jingying Liu","doi":"10.1093/hr/uhag058","DOIUrl":"https://doi.org/10.1093/hr/uhag058","url":null,"abstract":"Salvia miltiorrhiza, a medicinal plant of high value, faces significant yield and quality losses due to salt stress. Identifying salt tolerance genes is therefore essential for breeding resilient varieties. Gibberellin (GA) metabolism and signaling are modulated by diverse factors, with GA 2-oxidase (GA2ox) playing a key role in stress adaptation by inactivating GA and fine-tuning growth under adverse conditions. In this work, we identified 12 GA2ox genes in S. miltiorrhiza and generated a SmGA2ox4 transgenic line. Heterologous expression in Arabidopsis thaliana improved salt tolerance through enhanced germination, root growth, antioxidant activity, and stress-related physiological markers. Similar results were observed in transgenic hairy roots of S. miltiorrhiza. HPLC analysis further showed that SmGA2ox4 overexpression promoted tanshinone accumulation but suppressed salvianolic acid biosynthesis, whereas RNAi-mediated silencing had the opposite effect. Thus, SmGA2ox4 acts as a dual-function regulator, enhancing both salt tolerance and tanshinone production. This study establishes a novel link between GA2ox-mediated stress response and secondary metabolism in S. miltiorrhiza, providing a basis for engineering stress-resistant, high-quality varieties.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"119 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147287555","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}
Luisa Carrégalo-Ríos, Carlos Molina-Santiago, María V Berlanga-Clavero, Daniel Petras, Jesús Hierrezuelo, Mónica Pineda, Juan M Alba, Antonio de Vicente, Matilde Barón-Ayala, Pieter C Dorrestein, Diego Romero
Early microbial seed priming is conceived to improve crop resilience, yet it remains unclear whether plants can discriminate among closely related beneficial strains and integrate dose-dependent microbial cues. We primed melon (Cucumis melo) seeds with two phylogenetically similar Bacillus strains (B. subtilis NCIB3610 and B. velezensis FZB42) and combined transcriptomic, metabolomic, and physiological analyses across development. Despite comparable colonization, the strains provoked contrasting host programs and distinct dose responses. B. subtilis promoted radicle elongation, chloroplastic starch storage and drought tolerance regardless of inoculum level, together with L-tryptophan and palatinose accumulation. By contrast, B. velezensis displayed a clear dose effect: low inoculum sustained normal radicle growth, whereas high inoculum transiently repressed it, coinciding with suppression of allene oxide synthase, genes related with proteasome complex, and enrichment of flavonoids and glutathione in leaves. Chemical assays showed that radicle inhibition depends on the synergistic action of surfactin, produced by both strains, and bacillomycin D, an iturin-type lipopeptide specific to FZB42. This synergy explains the strain-specific lipopeptide repertoire to the dose-dependent growth response. Although their early trajectories diverged, both primings converged on enhanced aboveground stress resilience. 3610-primed plants restricted Botrytis cinerea via caffeic- and rosmarinic-acid accumulation, whereas FZB42-primed plants curtailed jasmonate-sensitive Tetranychus urticae mites through jasmonic acid (JA)-pathway modulation. Our results demonstrate that melon perceives inoculum dose and microbial identity, translating them into distinct metabolic and defense programs that converge on stress resilience. These mechanistic insights (linking lipopeptide fingerprints, sentinel metabolites and defense transcripts) provide a framework for precision seed treatments in horticultural crops.
{"title":"Early seed priming with closely related Bacillus strains induces divergent physiological and defense responses in melon","authors":"Luisa Carrégalo-Ríos, Carlos Molina-Santiago, María V Berlanga-Clavero, Daniel Petras, Jesús Hierrezuelo, Mónica Pineda, Juan M Alba, Antonio de Vicente, Matilde Barón-Ayala, Pieter C Dorrestein, Diego Romero","doi":"10.1093/hr/uhag053","DOIUrl":"https://doi.org/10.1093/hr/uhag053","url":null,"abstract":"Early microbial seed priming is conceived to improve crop resilience, yet it remains unclear whether plants can discriminate among closely related beneficial strains and integrate dose-dependent microbial cues. We primed melon (Cucumis melo) seeds with two phylogenetically similar Bacillus strains (B. subtilis NCIB3610 and B. velezensis FZB42) and combined transcriptomic, metabolomic, and physiological analyses across development. Despite comparable colonization, the strains provoked contrasting host programs and distinct dose responses. B. subtilis promoted radicle elongation, chloroplastic starch storage and drought tolerance regardless of inoculum level, together with L-tryptophan and palatinose accumulation. By contrast, B. velezensis displayed a clear dose effect: low inoculum sustained normal radicle growth, whereas high inoculum transiently repressed it, coinciding with suppression of allene oxide synthase, genes related with proteasome complex, and enrichment of flavonoids and glutathione in leaves. Chemical assays showed that radicle inhibition depends on the synergistic action of surfactin, produced by both strains, and bacillomycin D, an iturin-type lipopeptide specific to FZB42. This synergy explains the strain-specific lipopeptide repertoire to the dose-dependent growth response. Although their early trajectories diverged, both primings converged on enhanced aboveground stress resilience. 3610-primed plants restricted Botrytis cinerea via caffeic- and rosmarinic-acid accumulation, whereas FZB42-primed plants curtailed jasmonate-sensitive Tetranychus urticae mites through jasmonic acid (JA)-pathway modulation. Our results demonstrate that melon perceives inoculum dose and microbial identity, translating them into distinct metabolic and defense programs that converge on stress resilience. These mechanistic insights (linking lipopeptide fingerprints, sentinel metabolites and defense transcripts) provide a framework for precision seed treatments in horticultural crops.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"345 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147279058","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 one of the most economically important vegetable crops worldwide. Fruit quality is a critical determinant of consumer preference and market value, with color being the primary visual trait. While carotenoids impart red pigmentation, anthocyanins enable the accumulation of deep purple and blue hues. Although anthocyanins have been widely studied, a comprehensive understanding of their biosynthesis and regulation in tomato is still lacking. This review therefore synthesizes current knowledge to outline the molecular mechanisms underlying these processes. We highlight the central role of the MYB–bHLH–WD40 (MBW) transcriptional activation complex. Additionally, we discuss the multi-layered regulatory network involving other transcription factors, such as the bZIP family members SlHY5 and SlAREB1, BBX proteins, and others. Furthermore, we elaborate on post-transcriptional and post-translational regulatory mechanisms, which fine-tune anthocyanin accumulation. Finally, we outline current challenges and future directions for enhancing tomato anthocyanins. This review serves the dual purpose of providing an updated theoretical foundation for genetic improvement in tomato and offering a regulatory framework applicable to other horticultural crops.
{"title":"Recent progress in unraveling the molecular mechanisms of anthocyanin biosynthesis and regulation in tomato","authors":"Yuanyuan Kong, Aiyin Cui, Xuemei Hou, Yali Zhu, Weibiao Liao","doi":"10.1093/hr/uhag057","DOIUrl":"https://doi.org/10.1093/hr/uhag057","url":null,"abstract":"Tomato (Solanum lycopersicum) is one of the most economically important vegetable crops worldwide. Fruit quality is a critical determinant of consumer preference and market value, with color being the primary visual trait. While carotenoids impart red pigmentation, anthocyanins enable the accumulation of deep purple and blue hues. Although anthocyanins have been widely studied, a comprehensive understanding of their biosynthesis and regulation in tomato is still lacking. This review therefore synthesizes current knowledge to outline the molecular mechanisms underlying these processes. We highlight the central role of the MYB–bHLH–WD40 (MBW) transcriptional activation complex. Additionally, we discuss the multi-layered regulatory network involving other transcription factors, such as the bZIP family members SlHY5 and SlAREB1, BBX proteins, and others. Furthermore, we elaborate on post-transcriptional and post-translational regulatory mechanisms, which fine-tune anthocyanin accumulation. Finally, we outline current challenges and future directions for enhancing tomato anthocyanins. This review serves the dual purpose of providing an updated theoretical foundation for genetic improvement in tomato and offering a regulatory framework applicable to other horticultural crops.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"99 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147279838","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}
Chang An, Bingrui Wang, Denglin Li, Junzhang Li, Yongbin Lu, Yixin Yao, Yanxiang Lin, Lin Lu, Yan Cheng, Chongrong Ke, Zongshen Zhang, Ping Zheng, Yuan Qin
Clinacanthus nutans is a traditional medicinal plant widely used in Southeast Asia for treating inflammation, viral infections, and cancer. However, its molecular basis remains poorly understood. In this study, the first chromosome-scale genome of C. nutans (731.61 Mbp) was assembled, with 93.76% anchored to 18 pseudochromosomes. Repetitive elements constituted 69.05% of the genome, predominantly long terminal repeat (LTR) retrotransposons. Phylogenomic and synonymous substitution rate (Ks) analyses revealed a Lamiales-wide whole-genome duplication (WGD) event, followed by extensive chromosomal rearrangements. Gene family expansion analysis showed that segmental and dispersed duplications were the primary drivers of enzyme-coding genes (EGs) expansion involved in the flavonoid and triterpenoid pathways. Integrated transcriptomic and metabolomic analyses across five organs revealed distinct organ-specific expression and metabolite profiles. Genes exhibited pronounced differential expression between leaves and roots, with enrichment in flavonoid and triterpenoid biosynthetic pathways, highlighting functional divergence and metabolic specialization. Flavonoids were enriched in aerial tissues, whereas triterpenoids accumulated in roots. Weighted gene co-expression network analysis (WGCNA) identified key EGs (e.g., CHS, CHI, OSC) and core transcription factors (TFs) (e.g., MYB, bHLH, WRKY) potentially involved in organ-specific metabolic regulation. These findings suggest a coordinated transcriptional-metabolic regulatory framework underlying the specialized functions of different tissues. This work provides valuable genomic resources and mechanistic insights into the biosynthesis and regulation of bioactive compounds in C. nutans, thereby facilitating future research and molecular breeding of this important ethnomedicinal plant.
{"title":"From folklore to explore: integrating genomic and multi-omics data for Clinacanthus nutans provides insights into the evolution and organ-specific therapeutic basis","authors":"Chang An, Bingrui Wang, Denglin Li, Junzhang Li, Yongbin Lu, Yixin Yao, Yanxiang Lin, Lin Lu, Yan Cheng, Chongrong Ke, Zongshen Zhang, Ping Zheng, Yuan Qin","doi":"10.1093/hr/uhag037","DOIUrl":"https://doi.org/10.1093/hr/uhag037","url":null,"abstract":"Clinacanthus nutans is a traditional medicinal plant widely used in Southeast Asia for treating inflammation, viral infections, and cancer. However, its molecular basis remains poorly understood. In this study, the first chromosome-scale genome of C. nutans (731.61 Mbp) was assembled, with 93.76% anchored to 18 pseudochromosomes. Repetitive elements constituted 69.05% of the genome, predominantly long terminal repeat (LTR) retrotransposons. Phylogenomic and synonymous substitution rate (Ks) analyses revealed a Lamiales-wide whole-genome duplication (WGD) event, followed by extensive chromosomal rearrangements. Gene family expansion analysis showed that segmental and dispersed duplications were the primary drivers of enzyme-coding genes (EGs) expansion involved in the flavonoid and triterpenoid pathways. Integrated transcriptomic and metabolomic analyses across five organs revealed distinct organ-specific expression and metabolite profiles. Genes exhibited pronounced differential expression between leaves and roots, with enrichment in flavonoid and triterpenoid biosynthetic pathways, highlighting functional divergence and metabolic specialization. Flavonoids were enriched in aerial tissues, whereas triterpenoids accumulated in roots. Weighted gene co-expression network analysis (WGCNA) identified key EGs (e.g., CHS, CHI, OSC) and core transcription factors (TFs) (e.g., MYB, bHLH, WRKY) potentially involved in organ-specific metabolic regulation. These findings suggest a coordinated transcriptional-metabolic regulatory framework underlying the specialized functions of different tissues. This work provides valuable genomic resources and mechanistic insights into the biosynthesis and regulation of bioactive compounds in C. nutans, thereby facilitating future research and molecular breeding of this important ethnomedicinal plant.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"52 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147279059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The genus Philodendron exhibits exceptional diversity and ornamental value, but the genetic and evolutionary mechanisms driving its speciation and trait variation remain largely unknown. In this study, we constructed a haplotype-resolved, near-complete genome of Philodendron tatei to investigate its evolutionary origins, resolve its phylogenomic placement within Araceae, reconstruct karyotype evolution, and explore genetic clusters and hybridization patterns within Philodendron cultivars. Additionally, the genetic and regulatory mechanisms underlying leaf color variation, a key horticultural trait, were explored. Phylogenomic analysis placed Philodendron within the Araceae family and provided insights into its karyotype evolution. Comparative genomic analyses identified five major genetic clusters across the genus, highlighting extensive hybridization and allele specific expression (ASE) as key contributors to Philodendron’s diversity. To investigate leaf color variation, variant mining and transcriptome profiling were conducted on samples with diverse pigmentation. Functional validation identified PtSGR1 as a critical regulator of pigmentation formation, with differences in promoter activity driving variation in leaf coloration. Overall, this study provides a comprehensive genomic framework for understanding Philodendron evolution and diversity, tracing the significant role of hybridization in shaping its speciation and identifying key genetic mechanisms underlying ornamental traits. These insights advance our understanding of plant evolution, contribute to horticultural innovation, and enhance the genetic resources available for studying this ecologically and economically important genus.
{"title":"Hybridization footprint and the mechanism of leaf color differences in philodendron cultivars","authors":"Jiaxuan Chen, Fangping LI, Cong Xu, Jieying Liu, Zhuangwei Hou, Zhilong Huang, Zenpeng Gan, Yuchen Mao, Xiaoran Yan, Haifei Hu, Zefu Wang, Shaokui Wang, HaiPing Fu, Suhong Bu","doi":"10.1093/hr/uhag041","DOIUrl":"https://doi.org/10.1093/hr/uhag041","url":null,"abstract":"The genus Philodendron exhibits exceptional diversity and ornamental value, but the genetic and evolutionary mechanisms driving its speciation and trait variation remain largely unknown. In this study, we constructed a haplotype-resolved, near-complete genome of Philodendron tatei to investigate its evolutionary origins, resolve its phylogenomic placement within Araceae, reconstruct karyotype evolution, and explore genetic clusters and hybridization patterns within Philodendron cultivars. Additionally, the genetic and regulatory mechanisms underlying leaf color variation, a key horticultural trait, were explored. Phylogenomic analysis placed Philodendron within the Araceae family and provided insights into its karyotype evolution. Comparative genomic analyses identified five major genetic clusters across the genus, highlighting extensive hybridization and allele specific expression (ASE) as key contributors to Philodendron’s diversity. To investigate leaf color variation, variant mining and transcriptome profiling were conducted on samples with diverse pigmentation. Functional validation identified PtSGR1 as a critical regulator of pigmentation formation, with differences in promoter activity driving variation in leaf coloration. Overall, this study provides a comprehensive genomic framework for understanding Philodendron evolution and diversity, tracing the significant role of hybridization in shaping its speciation and identifying key genetic mechanisms underlying ornamental traits. These insights advance our understanding of plant evolution, contribute to horticultural innovation, and enhance the genetic resources available for studying this ecologically and economically important genus.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"11 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146222836","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}
Papaya is a major tropical fruit crop with notable nutritional and economic value, yet its genetic improvement through modern breeding technologies faces substantial challenges. The traditional tissue culture process is both labor-intensive and time-consuming, causing gene editing advancements in papaya to lag behind those in other crops. To overcome these obstacles, we developed a tissue culture–independent hairy root system in papaya, which enables efficient gene editing and significantly enhances the application and development of editing tools. This innovative platform allows for the pre-assessment of editing efficiency and supports the establishment of adenine base editor (ABE) and cytosine base editor (CBE) tools in papaya, thereby mitigating the high failure costs associated with the lengthy cycle of conventional genetic transformation. Utilizing this system, we pre-tested sgRNA activity and achieved high editing efficiency of CpWIP3 during stable transformation. Additionally, through promoter screening, we successfully developed ABE and CBE tools, marking the first precise single-nucleotide editing system in papaya. This gene-editing system provides a crucial platform for advancing functional genomics and accelerating precision breeding in papaya.
{"title":"Establishing efficient multi-gene editing tools for papaya","authors":"Bowei Wang, Xuesong Cao, Zeng Lin, Yiting Zhuang, Guihua Yang, Jian-Kang Zhu, Ray Ming, Jingjing Yue","doi":"10.1093/hr/uhag049","DOIUrl":"https://doi.org/10.1093/hr/uhag049","url":null,"abstract":"Papaya is a major tropical fruit crop with notable nutritional and economic value, yet its genetic improvement through modern breeding technologies faces substantial challenges. The traditional tissue culture process is both labor-intensive and time-consuming, causing gene editing advancements in papaya to lag behind those in other crops. To overcome these obstacles, we developed a tissue culture–independent hairy root system in papaya, which enables efficient gene editing and significantly enhances the application and development of editing tools. This innovative platform allows for the pre-assessment of editing efficiency and supports the establishment of adenine base editor (ABE) and cytosine base editor (CBE) tools in papaya, thereby mitigating the high failure costs associated with the lengthy cycle of conventional genetic transformation. Utilizing this system, we pre-tested sgRNA activity and achieved high editing efficiency of CpWIP3 during stable transformation. Additionally, through promoter screening, we successfully developed ABE and CBE tools, marking the first precise single-nucleotide editing system in papaya. This gene-editing system provides a crucial platform for advancing functional genomics and accelerating precision breeding in papaya.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"280 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146222835","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}
Lennard Garcia-de Heer, Jos Mieog, Adam Burn, Matthew Nolan, Lei Liu, Stephen Siazon, Tobias Kretzschmar
Cannabis sativa is a wind-pollinated, predominantly dioecious and outcrossing crop associated with high levels of genetic variability even within a single cultivar. As such, seed-grown crops are often constrained by variability issues, decreasing production efficiency and product consistency. F1 hybrid seed technology offers great potential to address these limitations by generating genetically uniform populations from a cross of two inbred parental lines. In C. sativa, single seed descent is currently the most viable method to produce these homozygous parental lines necessary for F1 hybrid seed production. This study exemplifies the potential of single-seed descent coupled with chemically induced sex reversion to produce fully homozygous lines and its subsequent application in creating five F1 hybrid accessions. Up to six rounds of single seed descent were performed in an 18-month period on 16 different lines, highlighting the speed of methodology. Inbreeding through XY males was most successful and offered the greatest advantages of the lines assessed. The F1 hybrid lines were statistically more uniform than the inbred or original lines, and more vigorous than the inbred lines, with F1 lines increasing seed yield between 3.9-155% when compared to their mid-parents indicating the potential to exploit heterosis. Chemotype stability was achieved in some F1 hybrid lines, showing that seed-grown cannabinoid crops would be possible in some contexts using F1 hybrid methodology, paving the way for the validation of this breeding technique in field settings and highlighting a path toward commercial hybrid seed systems in C. sativa.
{"title":"Weeding out variability: A proof-of-concept for producing uniform F1 hybrid Cannabis sativa L. using single seed descent","authors":"Lennard Garcia-de Heer, Jos Mieog, Adam Burn, Matthew Nolan, Lei Liu, Stephen Siazon, Tobias Kretzschmar","doi":"10.1093/hr/uhag038","DOIUrl":"https://doi.org/10.1093/hr/uhag038","url":null,"abstract":"Cannabis sativa is a wind-pollinated, predominantly dioecious and outcrossing crop associated with high levels of genetic variability even within a single cultivar. As such, seed-grown crops are often constrained by variability issues, decreasing production efficiency and product consistency. F1 hybrid seed technology offers great potential to address these limitations by generating genetically uniform populations from a cross of two inbred parental lines. In C. sativa, single seed descent is currently the most viable method to produce these homozygous parental lines necessary for F1 hybrid seed production. This study exemplifies the potential of single-seed descent coupled with chemically induced sex reversion to produce fully homozygous lines and its subsequent application in creating five F1 hybrid accessions. Up to six rounds of single seed descent were performed in an 18-month period on 16 different lines, highlighting the speed of methodology. Inbreeding through XY males was most successful and offered the greatest advantages of the lines assessed. The F1 hybrid lines were statistically more uniform than the inbred or original lines, and more vigorous than the inbred lines, with F1 lines increasing seed yield between 3.9-155% when compared to their mid-parents indicating the potential to exploit heterosis. Chemotype stability was achieved in some F1 hybrid lines, showing that seed-grown cannabinoid crops would be possible in some contexts using F1 hybrid methodology, paving the way for the validation of this breeding technique in field settings and highlighting a path toward commercial hybrid seed systems in C. sativa.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"35 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146215621","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}
Histone modification is an important part of epigenetic research and plays a significant role in maintaining the stability of eukaryotic genomes, regulating gene expression and chromatin remodelling. Histone methylation is one of the most complex modification forms in epigenetic regulation, which can occur on specific lysine or arginine residues at the tail of histones. Its biological function depends on the degree of methylation (me/me2/me3). Histone methylation involves multiple links, such as “writer”, “reader”, and “eraser” enzymes, and can activate or inhibit gene transcription by recruiting various downstream effector proteins. As molecular biology techniques have advanced, significant progress has been made in fundamental research on histone methylations in plants, and researchers have gained insights into its complex multilevel regulatory mechanisms. This review systematically summarizes recent advances in the roles of histone methylation in regulating plant dormancy and germination, flowering and senescence, as well as stress responses, and proposes a cross-regulatory model integrating histone methylation with multiple signalling pathways. These insights provide a theoretical foundation for the application of epigenetic breeding strategies in horticultural crops, with the goal of enhancing stress resistance, yield, and stress tolerance.
{"title":"Dynamic regulatory mechanisms of histone methylation in plant development and environmental adaptation","authors":"Sa Rina, Fan Xinyue, Sun Hongmei","doi":"10.1093/hr/uhag047","DOIUrl":"https://doi.org/10.1093/hr/uhag047","url":null,"abstract":"Histone modification is an important part of epigenetic research and plays a significant role in maintaining the stability of eukaryotic genomes, regulating gene expression and chromatin remodelling. Histone methylation is one of the most complex modification forms in epigenetic regulation, which can occur on specific lysine or arginine residues at the tail of histones. Its biological function depends on the degree of methylation (me/me2/me3). Histone methylation involves multiple links, such as “writer”, “reader”, and “eraser” enzymes, and can activate or inhibit gene transcription by recruiting various downstream effector proteins. As molecular biology techniques have advanced, significant progress has been made in fundamental research on histone methylations in plants, and researchers have gained insights into its complex multilevel regulatory mechanisms. This review systematically summarizes recent advances in the roles of histone methylation in regulating plant dormancy and germination, flowering and senescence, as well as stress responses, and proposes a cross-regulatory model integrating histone methylation with multiple signalling pathways. These insights provide a theoretical foundation for the application of epigenetic breeding strategies in horticultural crops, with the goal of enhancing stress resistance, yield, and stress tolerance.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"4 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146222837","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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