Shina Sasi, Saranya Krishnan, Martin Kottackal, Khaled M A Amiri
Nucellar apomixis is truly clonal and is a powerful tool for broadening the genetic base of crops. Black pepper (Piper nigrum L.), the “King of Spices” is difficult to improve through conventional breeding. Although transgenesis and genome editing are prime strategies for rapid crop improvement, recalcitrance hinders genetic modifications. Here, we report a highly efficient Agrobacterium-mediated procedure for generating genetically modified black pepper plants using nucellar apomixis-derived embryos of the varieties Sreekara and Karimunda, with a 99% survival rate. Both Agrobacterium tumefaciens and A. rhizogenes were efficient in transformation, and the AGL1 strain harboring the plasmid with mgfp achieved >90% frequency following 20 min in the infection medium, 30 s sonication, 10 min vacuum infiltration, and four days of co-cultivation. Sugar type determined embryonal taproot development and soil establishment. Glucose-supplemented medium produced plantlets with well-developed root systems that displayed a high expression of PnPIN2. Transgenic plantlets survival ex vitro from glucose-supplemented liquid medium was 99%. The genome-editing efficiency of Pds using CRISPR/Cas9 was 89%. Agroinfiltration of black pepper in this study is useful for high-throughput screening of disease resistance. Composite plants of black pepper generated at >60% efficacy is an easy strategy to develop plants expressing disease-resistant genes in roots to reduce yield loss, especially by root-rot. This study demonstrates that black pepper is an easy-to-transform crop, which reinforces speedy trait development through genetic modifications. Scale-up using temporary immersion bioreactors in this study fast-track high throughput accomplishment of untransformed/transformed/genome edited plants empower the market demand for black pepper.
{"title":"Reducing recalcitrance of black pepper to Agrobacterium -mediated transformation: an efficient way through nucellar apomixis to establish transgenic and genome-edited plants at high frequency and scale-up through bioreactor","authors":"Shina Sasi, Saranya Krishnan, Martin Kottackal, Khaled M A Amiri","doi":"10.1093/hr/uhag067","DOIUrl":"https://doi.org/10.1093/hr/uhag067","url":null,"abstract":"Nucellar apomixis is truly clonal and is a powerful tool for broadening the genetic base of crops. Black pepper (Piper nigrum L.), the “King of Spices” is difficult to improve through conventional breeding. Although transgenesis and genome editing are prime strategies for rapid crop improvement, recalcitrance hinders genetic modifications. Here, we report a highly efficient Agrobacterium-mediated procedure for generating genetically modified black pepper plants using nucellar apomixis-derived embryos of the varieties Sreekara and Karimunda, with a 99% survival rate. Both Agrobacterium tumefaciens and A. rhizogenes were efficient in transformation, and the AGL1 strain harboring the plasmid with mgfp achieved >90% frequency following 20 min in the infection medium, 30 s sonication, 10 min vacuum infiltration, and four days of co-cultivation. Sugar type determined embryonal taproot development and soil establishment. Glucose-supplemented medium produced plantlets with well-developed root systems that displayed a high expression of PnPIN2. Transgenic plantlets survival ex vitro from glucose-supplemented liquid medium was 99%. The genome-editing efficiency of Pds using CRISPR/Cas9 was 89%. Agroinfiltration of black pepper in this study is useful for high-throughput screening of disease resistance. Composite plants of black pepper generated at >60% efficacy is an easy strategy to develop plants expressing disease-resistant genes in roots to reduce yield loss, especially by root-rot. This study demonstrates that black pepper is an easy-to-transform crop, which reinforces speedy trait development through genetic modifications. Scale-up using temporary immersion bioreactors in this study fast-track high throughput accomplishment of untransformed/transformed/genome edited plants empower the market demand for black pepper.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"13 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147314877","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}
Ginkgo biloba is a singular and relict gymnosperm indigenous to China. Its distinctive fleshy episperm is rich in unique metabolites, ginkgolic acids, which protect the developing seed from biotic stresses. The unique nature of the tissue and its metabolites has made it highly challenging to elucidate the molecular and cellular mechanisms governing ginkgolic acid biosynthesis and regulation. In this study, we performed the mass spectrometry imaging of G. biloba seed, revealing that ginkgolic acids primarily accumulate in the secretory cavities of the episperm. We constructed a single-cell expression atlas of the G. biloba episperm, and identifying seven cellular types: meristem cells, subepidermal cells, lignified cells, trancheid cells, parenchymal cells, secretory cavity cells, and epidermis cells. Based on the analysis of upregulated gene expression in secretory cavity cells, pseudotime analysis of cell differentiation and gene expression trajectory analysis, we precisely identified the key enzyme-encoding genes highly associated with ginkgolic acid biosynthesis. This approach elucidated the cellular and molecular mechanisms underlying secretory cell differentiation, secretory cavity formation, and ginkgolic acid biosynthesis and accumulation in response to exogenous jasmonic acid induction. By constructing a molecular interaction network, it was determined that the GbWRKY35, encoded by Gb_25334, is the core transcription factor. We further identified the signaling proteins that interact with GbWRKY35, confirming its central positive regulatory role in ginkgolic acid biosynthesis. As a core transcription factor, GbWRKY35 regulates ginkgolic acid biosynthesis through stimulating the expression of GbAAE16.This study provides the first spatially resolved investigation into the molecular and cellular regulatory mechanisms of ginkgolic acid biosynthesis in the episperm under jasmonic acid induction.
{"title":"Single-nucleus sequencing and spatial metabolomics analysis reveal the regulatory mechanism of ginkgolic acid biosynthesis in the episperm of Ginkgo Biloba","authors":"Zhi Feng, Zhi Yao, Qiye Wang, Bei Zhang, Hui Wang, Yuanqing Wang, Binlin Ai, Xingyu Zhang, Hailan Jiang, Yifan Xiao, Yiqiang Wang, Meng Li","doi":"10.1093/hr/uhag064","DOIUrl":"https://doi.org/10.1093/hr/uhag064","url":null,"abstract":"Ginkgo biloba is a singular and relict gymnosperm indigenous to China. Its distinctive fleshy episperm is rich in unique metabolites, ginkgolic acids, which protect the developing seed from biotic stresses. The unique nature of the tissue and its metabolites has made it highly challenging to elucidate the molecular and cellular mechanisms governing ginkgolic acid biosynthesis and regulation. In this study, we performed the mass spectrometry imaging of G. biloba seed, revealing that ginkgolic acids primarily accumulate in the secretory cavities of the episperm. We constructed a single-cell expression atlas of the G. biloba episperm, and identifying seven cellular types: meristem cells, subepidermal cells, lignified cells, trancheid cells, parenchymal cells, secretory cavity cells, and epidermis cells. Based on the analysis of upregulated gene expression in secretory cavity cells, pseudotime analysis of cell differentiation and gene expression trajectory analysis, we precisely identified the key enzyme-encoding genes highly associated with ginkgolic acid biosynthesis. This approach elucidated the cellular and molecular mechanisms underlying secretory cell differentiation, secretory cavity formation, and ginkgolic acid biosynthesis and accumulation in response to exogenous jasmonic acid induction. By constructing a molecular interaction network, it was determined that the GbWRKY35, encoded by Gb_25334, is the core transcription factor. We further identified the signaling proteins that interact with GbWRKY35, confirming its central positive regulatory role in ginkgolic acid biosynthesis. As a core transcription factor, GbWRKY35 regulates ginkgolic acid biosynthesis through stimulating the expression of GbAAE16.This study provides the first spatially resolved investigation into the molecular and cellular regulatory mechanisms of ginkgolic acid biosynthesis in the episperm under jasmonic acid induction.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"97 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147314878","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 circadian clock enables plants to synchronize physiological and developmental processes with daily and seasonal light fluctuations. In horticultural crops, this endogenous oscillator interacts with photoperiod, light quality, and light intensity to coordinate flowering, growth, metabolism, and stress adaptation. Photoperiodic control, mediated largely by the conserved CONSTANS (CO)–FLOWERING LOCUS T (FT) module, governs flowering transitions and vegetative–reproductive balance in horticultural crops, such as strawberry, chrysanthemum, cucumber, tomato, and potato. Spectral composition, particularly red/far-red and blue light perceived through phytochromes and cryptochromes, reshapes circadian amplitude and phase to regulate photosynthesis, morphogenesis, and secondary metabolism. Meanwhile, light intensity adjusts oscillator robustness and energy allocation, influencing rhythmic stability under controlled-environment cultivation. The emerging research topics such as on species-specific clock diversity, circadian regulation of quality traits, and precision lighting strategies aligned with rhythmic principles were also discussed. Analyzing the interaction between light signals and the biological clock will help deepen our understanding of the time regulation mechanism in horticulture plants, and can provide a basis for designing optimized periodic cultivation systems in horticulture, thereby improving yield and quality of horticultural crops. In this review, we will summarize the research findings on how light environments regulate the circadian rhythms of horticultural plants, as well as their potential applications in horticulture.
{"title":"Integrated circadian regulation in horticultural plants: light-environment mechanisms governing growth and development","authors":"Zhi-Hang Hu, Nan Zhang, Ting Huang, Chen Chen, Jing Zhuang, Ai-Sheng Xiong","doi":"10.1093/hr/uhag056","DOIUrl":"https://doi.org/10.1093/hr/uhag056","url":null,"abstract":"The circadian clock enables plants to synchronize physiological and developmental processes with daily and seasonal light fluctuations. In horticultural crops, this endogenous oscillator interacts with photoperiod, light quality, and light intensity to coordinate flowering, growth, metabolism, and stress adaptation. Photoperiodic control, mediated largely by the conserved CONSTANS (CO)–FLOWERING LOCUS T (FT) module, governs flowering transitions and vegetative–reproductive balance in horticultural crops, such as strawberry, chrysanthemum, cucumber, tomato, and potato. Spectral composition, particularly red/far-red and blue light perceived through phytochromes and cryptochromes, reshapes circadian amplitude and phase to regulate photosynthesis, morphogenesis, and secondary metabolism. Meanwhile, light intensity adjusts oscillator robustness and energy allocation, influencing rhythmic stability under controlled-environment cultivation. The emerging research topics such as on species-specific clock diversity, circadian regulation of quality traits, and precision lighting strategies aligned with rhythmic principles were also discussed. Analyzing the interaction between light signals and the biological clock will help deepen our understanding of the time regulation mechanism in horticulture plants, and can provide a basis for designing optimized periodic cultivation systems in horticulture, thereby improving yield and quality of horticultural crops. In this review, we will summarize the research findings on how light environments regulate the circadian rhythms of horticultural plants, as well as their potential applications in horticulture.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"12 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147287571","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}
Cucumis sativus L., commonly known as cucumber, is an important vegetable crop worldwide, with China as the largest producer, particularly of the North and South China types. While extensive genomic research has focused on the North China type, especially the Chinese Long 9930, studies on the South China type remain limited. In this study, we assembled high-quality genomes of two widely cultivated and representative parent varieties: S36 (North China type) and H19 (South China type), and conducted mutagenesis analyses. Comparative genome analysis revealed a large number of structural variants between two North China types and two South China types, with many of the affected genes showing strong homology to known functional loci, potentially contributing to phenotypic divergence. We also constructed an EMS mutant library through the mutagenesis of S36 and identified a gene that encodes chlorophyll oxidase, demonstrating the method’s effectiveness for rapid gene discovery. In conclusion, this study provides valuable insights into the classification and evolution of cucumber, highlighting the promising potential of forward genetic approaches in cucumber breeding.
{"title":"A comprehensive analysis of two Chinese cucumber genomes and a mutant population as resources for precision breeding","authors":"Jiaxi Han, Jingwei Wei, Weiliang Kong, Weili Miao, Lidong Zhang, Yuhe Li, Jiawang Li, Xin Li, Tao Lin, Hongyu Huang","doi":"10.1093/hr/uhaf284","DOIUrl":"https://doi.org/10.1093/hr/uhaf284","url":null,"abstract":"Cucumis sativus L., commonly known as cucumber, is an important vegetable crop worldwide, with China as the largest producer, particularly of the North and South China types. While extensive genomic research has focused on the North China type, especially the Chinese Long 9930, studies on the South China type remain limited. In this study, we assembled high-quality genomes of two widely cultivated and representative parent varieties: S36 (North China type) and H19 (South China type), and conducted mutagenesis analyses. Comparative genome analysis revealed a large number of structural variants between two North China types and two South China types, with many of the affected genes showing strong homology to known functional loci, potentially contributing to phenotypic divergence. We also constructed an EMS mutant library through the mutagenesis of S36 and identified a gene that encodes chlorophyll oxidase, demonstrating the method’s effectiveness for rapid gene discovery. In conclusion, this study provides valuable insights into the classification and evolution of cucumber, highlighting the promising potential of forward genetic approaches in cucumber breeding.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"22 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147287556","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}
Apple Valsa canker (AVC), a disease instigated by Valsa mali (syn. Cytospora mali), poses a significant global threat to apple cultivation. Throughout its infection process, V. mali introduces an array of effector proteins into the host cells aimed at undermining the host immune defenses. The exact molecular mechanisms through which these effectors manipulate host transcription factors (TFs) to promote pathogenesis are not fully understood. This study identifies a ribonuclease T2-like effector, VmRnt2, that notably inhibits INF1-triggered cell death, chitin-induced reactive oxygen species (ROS) bursts, and callose deposition. Knockout of the VmRnt2 gene markedly reduced the virulence of V. mali, without impacting fungal growth or spore production. Conversely, heterologous expression of VmRnt2 in Nicotiana benthamiana and apple markedly enhanced susceptibility to infections by Sclerotinia sclerotiorum and V. mali, respectively, highlighting its pivotal role in facilitating pathogenicity. VmRnt2 was found to interact specifically with an apple TF, MdMYB44, which belongs to the myeloblastosis (MYB) family of proteins. Further functional assays revealed that overexpression of MdMYB44 in apple enhances resistance to V. mali. Additionally, MdMYB44 was shown to bind specifically to the promoter of the defense-related gene MdPR1A, subsequently activating its transcription. Importantly, during V. mali infection, VmRnt2 disrupts the DNA-binding activity of MdMYB44. Collectively, our results elucidate how V. mali employs VmRnt2 to compromise MdMYB44-mediated immune regulation, thereby facilitating the pathogen’s colonization of apple trees.
{"title":"The fungi effector VmRnt2 from Valsa Mali modulates host transcription factor to suppress immunity in apple","authors":"Hailong Liu, Pujiang Deng, Xing Gao, Shasha Chen, Qiyue Zhang, Liangsheng Xu, Lili Huang","doi":"10.1093/hr/uhag054","DOIUrl":"https://doi.org/10.1093/hr/uhag054","url":null,"abstract":"Apple Valsa canker (AVC), a disease instigated by Valsa mali (syn. Cytospora mali), poses a significant global threat to apple cultivation. Throughout its infection process, V. mali introduces an array of effector proteins into the host cells aimed at undermining the host immune defenses. The exact molecular mechanisms through which these effectors manipulate host transcription factors (TFs) to promote pathogenesis are not fully understood. This study identifies a ribonuclease T2-like effector, VmRnt2, that notably inhibits INF1-triggered cell death, chitin-induced reactive oxygen species (ROS) bursts, and callose deposition. Knockout of the VmRnt2 gene markedly reduced the virulence of V. mali, without impacting fungal growth or spore production. Conversely, heterologous expression of VmRnt2 in Nicotiana benthamiana and apple markedly enhanced susceptibility to infections by Sclerotinia sclerotiorum and V. mali, respectively, highlighting its pivotal role in facilitating pathogenicity. VmRnt2 was found to interact specifically with an apple TF, MdMYB44, which belongs to the myeloblastosis (MYB) family of proteins. Further functional assays revealed that overexpression of MdMYB44 in apple enhances resistance to V. mali. Additionally, MdMYB44 was shown to bind specifically to the promoter of the defense-related gene MdPR1A, subsequently activating its transcription. Importantly, during V. mali infection, VmRnt2 disrupts the DNA-binding activity of MdMYB44. Collectively, our results elucidate how V. mali employs VmRnt2 to compromise MdMYB44-mediated immune regulation, thereby facilitating the pathogen’s colonization of apple trees.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"53 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147287554","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}
Jiahu Zhang, Chen Wang, Haibo Wang, Ping He, Yuansheng Chang, Sen Wang, Wenyan Zheng, Nan Wang, Yongxu Wang, Qi Zou, Linguang Li, Xuesen Chen, Xiaowen He
The apple anthocyanin content is an important trait in apple breeding. Auxin, as an important plant hormone, plays significant roles in regulating the biosynthesis of anthocyanins. However, the molecular mechanism of how plants regulate auxin content and activity to affect anthocyanin accumulation remains unclear. In this study, through fruit anthocyanin content analysis and transcriptome sequencing of the hybrids derived from ‘Golden Delicious’ and ‘Fuji Nagafu No. 2’ crosses, a key gene for regulating apple anthocyanin accumulation, indole-3-acetic acid (IAA) methyltransferase (MdIAMT), was identified. Functional analyses showed that the apple calli and peel overexpressing MdIAMT accumulated more anthocyanin than that in Vec by regulating IAA homeostasis. Yeast two-hybrid assays, luciferase complementation imaging assays and co-immunoprecipitation assays revealed that MdCSN5, an important protein in light signal transduction, interacts with MdIAMT. More importantly, further research showed that the MdCSN5-MdIAMT module affected auxin signal transduction pathway by regulating IAA homeostasis, thus promoting anthocyanin accumulation. In summary, our findings elucidate a novel mechanism by which auxin-regulated anthocyanin accumulation via MdCSN5-MdIAMT module, deepening our knowledge of plant hormone signaling in anthocyanin biosynthesis.
{"title":"MdCSN5–MdIAMT module promotes anthocyanin accumulation by regulating IAA homeostasis in apple","authors":"Jiahu Zhang, Chen Wang, Haibo Wang, Ping He, Yuansheng Chang, Sen Wang, Wenyan Zheng, Nan Wang, Yongxu Wang, Qi Zou, Linguang Li, Xuesen Chen, Xiaowen He","doi":"10.1093/hr/uhaf290","DOIUrl":"https://doi.org/10.1093/hr/uhaf290","url":null,"abstract":"The apple anthocyanin content is an important trait in apple breeding. Auxin, as an important plant hormone, plays significant roles in regulating the biosynthesis of anthocyanins. However, the molecular mechanism of how plants regulate auxin content and activity to affect anthocyanin accumulation remains unclear. In this study, through fruit anthocyanin content analysis and transcriptome sequencing of the hybrids derived from ‘Golden Delicious’ and ‘Fuji Nagafu No. 2’ crosses, a key gene for regulating apple anthocyanin accumulation, indole-3-acetic acid (IAA) methyltransferase (MdIAMT), was identified. Functional analyses showed that the apple calli and peel overexpressing MdIAMT accumulated more anthocyanin than that in Vec by regulating IAA homeostasis. Yeast two-hybrid assays, luciferase complementation imaging assays and co-immunoprecipitation assays revealed that MdCSN5, an important protein in light signal transduction, interacts with MdIAMT. More importantly, further research showed that the MdCSN5-MdIAMT module affected auxin signal transduction pathway by regulating IAA homeostasis, thus promoting anthocyanin accumulation. In summary, our findings elucidate a novel mechanism by which auxin-regulated anthocyanin accumulation via MdCSN5-MdIAMT module, deepening our knowledge of plant hormone signaling in anthocyanin biosynthesis.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"19 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147287570","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}
Simeng Zhang, Ying Zhang, Jinpeng Bi, Jiayu Xu, Luming Tian, Xingguang Dong, Yang Yu, Wei Heng, Dan Qi, Hongliang Huo, Chao Liu, Ruiqing Pan, Xiang Yang, Chenxi Xu, Yufen Cao
Pear (Pyrus L.) is a fruit tree of global commercial importance. Its genetic relationships, evolutionary history, dissemination routes, and genetic determinants of most agronomic traits remain to be elucidated. We conducted whole-genome resequencing of 495 Pyrus accessions. Phylogenetic and demographic analyses resolved geographic groupings of the accessions, identifying the Yunnan–Guizhou Plateau as the putative dissemination center for cultivated P. pyrifolia and P. bretschneideri. Identification of two evolutionary bottlenecks provides insights into the population dynamics of pear species. Admixture and introgression analyses revealed both intra- and interspecific genetic exchanges, substantiating the complex emergence of cultivated populations. Genome-wide association study (GWAS) identified loci associated with nine crucial agronomic traits, together with eight candidate genes. The GWAS, molecular, and biochemical analyses suggested that PbeMADS25, PbeSPP, PbeDHQ-SDH, PbeARF2, PbePPO, PbePIN3, PbeCXE and PbeMYB38 participate in the regulation of number of stigmas and number of locules, number of stamens, young leaf color, sepal persistence, astringency, acidity, aroma and fruit skin color, respectively. Overexpression and metabonomic analysis of PbeCXE indicated that it affects the fruit aroma by affecting the balance between ester biosynthesis and substrate consumption. These findings expand our understanding of Pyrus evolution and provide a genomic foundation for genetic improvement of agronomic traits.
{"title":"Whole-genome resequencing of 495 Pyrus accessions provides insights into the genetics of agronomic traits, and evolutionary history of pear","authors":"Simeng Zhang, Ying Zhang, Jinpeng Bi, Jiayu Xu, Luming Tian, Xingguang Dong, Yang Yu, Wei Heng, Dan Qi, Hongliang Huo, Chao Liu, Ruiqing Pan, Xiang Yang, Chenxi Xu, Yufen Cao","doi":"10.1093/hr/uhag042","DOIUrl":"https://doi.org/10.1093/hr/uhag042","url":null,"abstract":"Pear (Pyrus L.) is a fruit tree of global commercial importance. Its genetic relationships, evolutionary history, dissemination routes, and genetic determinants of most agronomic traits remain to be elucidated. We conducted whole-genome resequencing of 495 Pyrus accessions. Phylogenetic and demographic analyses resolved geographic groupings of the accessions, identifying the Yunnan–Guizhou Plateau as the putative dissemination center for cultivated P. pyrifolia and P. bretschneideri. Identification of two evolutionary bottlenecks provides insights into the population dynamics of pear species. Admixture and introgression analyses revealed both intra- and interspecific genetic exchanges, substantiating the complex emergence of cultivated populations. Genome-wide association study (GWAS) identified loci associated with nine crucial agronomic traits, together with eight candidate genes. The GWAS, molecular, and biochemical analyses suggested that PbeMADS25, PbeSPP, PbeDHQ-SDH, PbeARF2, PbePPO, PbePIN3, PbeCXE and PbeMYB38 participate in the regulation of number of stigmas and number of locules, number of stamens, young leaf color, sepal persistence, astringency, acidity, aroma and fruit skin color, respectively. Overexpression and metabonomic analysis of PbeCXE indicated that it affects the fruit aroma by affecting the balance between ester biosynthesis and substrate consumption. These findings expand our understanding of Pyrus evolution and provide a genomic foundation for genetic improvement of agronomic traits.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"239 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147329712","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}
Yubing Yong, Heng Bi, Mingyue Li, Yichao Zhu, Qi Zhou, Wen Xing, Sixiang Zheng, Lin Zhang, Yingmin Lyu, Rong Song
Lilies (Lilium spp.) are globally important ornamental crops which are constrained by their narrow thermal tolerance range. However, tiger lily (L. lancifolium), a wild lily species, exhibits remarkable cold tolerance. Based on our previous findings, we proposed that LlR3MYB, an R3-MYB transcription factor (TF), confers cold tolerance via transcriptional regulation of flavonoid metabolism in tiger lily. Here, we revealed that LlR3MYB represents a unique CPC-type R3-MYB TF exhibiting a bifunctional role in flavonoid metabolism. Specifically, LlR3MYB suppresses anthocyanin biosynthesis while promoting non-anthocyanin flavonoid accumulation (i.e., flavonols, flavones, and chalcones) responding to cold stress. Overexpression of LlR3MYB in tobacco and tiger lily increased total flavonoid content but reduced anthocyanin levels, consistent with the upregulation of early biosynthesis genes (e.g., CHS and FLS) and repression of late biosynthesis genes (e.g., DFR and ANS) in the pathway. In contrast, silencing LlR3MYB in tiger lily reduced total flavonoid production, enhanced anthocyanin accumulation, and compromised cold resistance. Mechanistically, LlR3MYB can directly bind to the AC-I element (ACCTACC) and MBSI motif (CAACGGTT) in the LlCHS2 promoter and activating its transcription, with enhanced activation under low temperature conditions. Mutations of critical residues within the C1/C2 repressor motifs may endow LlR3MYB with this transcriptional activation function. Furthermore, LlDREB can directly bind to the DRE motif (ACCGAC) in the LlR3MYB promoter and activating its transcription in a low-temperature-dependent manner. Our findings uncover a branch-specific regulatory mechanism by which MYB TFs fine-tune flavonoid biosynthesis, highlighting their essential role in plant cold stress responses.
{"title":"LlR3MYB-mediated flavonoid biosynthesis confers cold stress tolerance in Lilium lancifolium through the LlDREB-LlCHS2 regulatory cascade","authors":"Yubing Yong, Heng Bi, Mingyue Li, Yichao Zhu, Qi Zhou, Wen Xing, Sixiang Zheng, Lin Zhang, Yingmin Lyu, Rong Song","doi":"10.1093/hr/uhag065","DOIUrl":"https://doi.org/10.1093/hr/uhag065","url":null,"abstract":"Lilies (Lilium spp.) are globally important ornamental crops which are constrained by their narrow thermal tolerance range. However, tiger lily (L. lancifolium), a wild lily species, exhibits remarkable cold tolerance. Based on our previous findings, we proposed that LlR3MYB, an R3-MYB transcription factor (TF), confers cold tolerance via transcriptional regulation of flavonoid metabolism in tiger lily. Here, we revealed that LlR3MYB represents a unique CPC-type R3-MYB TF exhibiting a bifunctional role in flavonoid metabolism. Specifically, LlR3MYB suppresses anthocyanin biosynthesis while promoting non-anthocyanin flavonoid accumulation (i.e., flavonols, flavones, and chalcones) responding to cold stress. Overexpression of LlR3MYB in tobacco and tiger lily increased total flavonoid content but reduced anthocyanin levels, consistent with the upregulation of early biosynthesis genes (e.g., CHS and FLS) and repression of late biosynthesis genes (e.g., DFR and ANS) in the pathway. In contrast, silencing LlR3MYB in tiger lily reduced total flavonoid production, enhanced anthocyanin accumulation, and compromised cold resistance. Mechanistically, LlR3MYB can directly bind to the AC-I element (ACCTACC) and MBSI motif (CAACGGTT) in the LlCHS2 promoter and activating its transcription, with enhanced activation under low temperature conditions. Mutations of critical residues within the C1/C2 repressor motifs may endow LlR3MYB with this transcriptional activation function. Furthermore, LlDREB can directly bind to the DRE motif (ACCGAC) in the LlR3MYB promoter and activating its transcription in a low-temperature-dependent manner. Our findings uncover a branch-specific regulatory mechanism by which MYB TFs fine-tune flavonoid biosynthesis, highlighting their essential role in plant cold stress responses.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"24 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147292724","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}
Dandan Lou, Yuyao Zhang, Pengchuan Wu, Hui Xiao, Fei Guo, Xingtan Zhang, Pu Wang, Weilong Kong
Horticultural crops, including fruits, vegetables, ornamental plants, and tea plants, are vital for economic and nutritional sustainability, yet their cultivation is severely hampered by abiotic stresses such as heat, cold, and salinity. The advent of the grapevine genome in 2007 initiated the genomic era for horticultural species. This milestone facilitated the use of genome-wide association studies (GWAS) to decode the complex phenotypic diversity of these crops. Unlike traditional methods, GWAS utilizes natural genetic diversity to identify quantitative trait loci linked to key traits, offering a high-resolution approach for dissecting traits such as stress resistance, quality, and yield. This review highlights the innovative workflows and technical advancements in GWAS applications for horticultural crops, covering aspects including population design, high-throughput phenotyping, sophisticated statistical modeling, and their applications in horticultural plants. Notably, the integration of multi-omics approaches has enhanced our understanding of the genetic mechanisms underlying critical horticultural traits. Future directions aim at harnessing technological innovations, cross-omics synthesis, and precision breeding strategies to optimize trait selection and expedite the development of resilient cultivars. Consequently, GWAS serves as a crucial bridge linking genomic variation to practical applications in horticultural improvement, enabling a paradigm shift towards predictive breeding and sustainable agricultural practices.
{"title":"Genome-wide Association Studies in Horticultural Crops: Decoding Genetic Diversity for Precision Breeding","authors":"Dandan Lou, Yuyao Zhang, Pengchuan Wu, Hui Xiao, Fei Guo, Xingtan Zhang, Pu Wang, Weilong Kong","doi":"10.1093/hr/uhag059","DOIUrl":"https://doi.org/10.1093/hr/uhag059","url":null,"abstract":"Horticultural crops, including fruits, vegetables, ornamental plants, and tea plants, are vital for economic and nutritional sustainability, yet their cultivation is severely hampered by abiotic stresses such as heat, cold, and salinity. The advent of the grapevine genome in 2007 initiated the genomic era for horticultural species. This milestone facilitated the use of genome-wide association studies (GWAS) to decode the complex phenotypic diversity of these crops. Unlike traditional methods, GWAS utilizes natural genetic diversity to identify quantitative trait loci linked to key traits, offering a high-resolution approach for dissecting traits such as stress resistance, quality, and yield. This review highlights the innovative workflows and technical advancements in GWAS applications for horticultural crops, covering aspects including population design, high-throughput phenotyping, sophisticated statistical modeling, and their applications in horticultural plants. Notably, the integration of multi-omics approaches has enhanced our understanding of the genetic mechanisms underlying critical horticultural traits. Future directions aim at harnessing technological innovations, cross-omics synthesis, and precision breeding strategies to optimize trait selection and expedite the development of resilient cultivars. Consequently, GWAS serves as a crucial bridge linking genomic variation to practical applications in horticultural improvement, enabling a paradigm shift towards predictive breeding and sustainable agricultural practices.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"49 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147292755","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}
Yiwei Zhou, Fang Wang, Xue Wei, Meixin Xiong, Ting Gao, Qin Wang, Lan Wang, Yunyi Yu, Rangcai Yu, Yanping Fan
Floral scent is a crucial quality trait in ornamental plants, yet research has been hampered by the lack of standardized sensory evaluation and the disconnect between genes, volatile compounds, and human perception. Hedychium is an excellent model for fragrance research due to its diverse fragrance types and rich volatile organic compound (VOC) profiles. This study establishes a sensory-omics framework to connect genetic pathways, VOC chemistry, and fragrance perception in Hedychium flowers. A multidisciplinary approach combined sensory panel analysis (developing a fragrance wheel), VOC profiling (HS–SPME–GC–MS and PTR–ToF–MS), transcriptomics, and functional characterization of key biosynthetic genes in 30 Hedychium accessions representing six fragrance types. Six distinct fragrance types were classified (e.g., strong floral, fruity), linked to specific VOC profiles (e.g., monoterpenoids, esters). PTR–ToF–MS validated rapid detection of key fragrance markers. Supervised partial least squares-discriminant analysis (PLS-DA) modeling of VOC signatures enabled fragrance-type classification and key variable selection. Transcriptomic analysis coupled with weighted gene co-expression network analysis (WGCNA) revealed two key gene modules—MEbrown (terpenoid-associated) and MEyellow (phenylpropanoid-associated)—that underlie fragrance variation. Functional validation through in vitro enzymatic assays and transient overexpression in tobacco leaves confirmed HcTPS1 as a eucalyptol synthase and HmBEAT1 as a benzyl acetate synthase. Collectively, these findings provide a comprehensive framework for Hedychium flowers, thereby elucidating the molecular and chemical basis of their sensory fragrance variation. The study delivers valuable genetic resources and a predictive model that establishes a foundation for the targeted breeding of floral fragrance in ornamental horticulture.
{"title":"From Fragrance Wheel to Functional Genes: A Multi-Omics Investigation into Fragrance Type Formation in Ornamental Hedychium Flowers","authors":"Yiwei Zhou, Fang Wang, Xue Wei, Meixin Xiong, Ting Gao, Qin Wang, Lan Wang, Yunyi Yu, Rangcai Yu, Yanping Fan","doi":"10.1093/hr/uhag063","DOIUrl":"https://doi.org/10.1093/hr/uhag063","url":null,"abstract":"Floral scent is a crucial quality trait in ornamental plants, yet research has been hampered by the lack of standardized sensory evaluation and the disconnect between genes, volatile compounds, and human perception. Hedychium is an excellent model for fragrance research due to its diverse fragrance types and rich volatile organic compound (VOC) profiles. This study establishes a sensory-omics framework to connect genetic pathways, VOC chemistry, and fragrance perception in Hedychium flowers. A multidisciplinary approach combined sensory panel analysis (developing a fragrance wheel), VOC profiling (HS–SPME–GC–MS and PTR–ToF–MS), transcriptomics, and functional characterization of key biosynthetic genes in 30 Hedychium accessions representing six fragrance types. Six distinct fragrance types were classified (e.g., strong floral, fruity), linked to specific VOC profiles (e.g., monoterpenoids, esters). PTR–ToF–MS validated rapid detection of key fragrance markers. Supervised partial least squares-discriminant analysis (PLS-DA) modeling of VOC signatures enabled fragrance-type classification and key variable selection. Transcriptomic analysis coupled with weighted gene co-expression network analysis (WGCNA) revealed two key gene modules—MEbrown (terpenoid-associated) and MEyellow (phenylpropanoid-associated)—that underlie fragrance variation. Functional validation through in vitro enzymatic assays and transient overexpression in tobacco leaves confirmed HcTPS1 as a eucalyptol synthase and HmBEAT1 as a benzyl acetate synthase. Collectively, these findings provide a comprehensive framework for Hedychium flowers, thereby elucidating the molecular and chemical basis of their sensory fragrance variation. The study delivers valuable genetic resources and a predictive model that establishes a foundation for the targeted breeding of floral fragrance in ornamental horticulture.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"19 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147292725","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：