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园艺研究（英文）
园艺研究（英文）
园艺研究（英文）/Journal Horticulture ResearchCSCDCSTPCDSCI
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    A 49-bp deletion of PmAP2L results in a double flower phenotype in Prunus mume

    Weichao LiuTangchun ZhengLike QiuXiaoyu Guo...
    131-147页
    查看更多>>摘要：The double flower is an important trait with substantial ornamental value.While mutations in PETALOSA TOE-type or AG(AGAMOUS)genes play a crucial role in enhancing petal number in ornamental plants,the complete mechanism underlying the formation of double flowers remains to be fully elucidated.Through the application of bulked segregant analysis(BSA),we identified a novel gene,APETALA2-like(PmAP2L),characterized by a 49-bp deletion in double-flowered Prunus mume.β-Glucuronidase(GUS)staining and luciferase reporter assays confirmed that the 49-bp deletion in PmAP2L reduced its binding with Pmu-miRNA172a.Phylogenetic analysis and microsynteny analysis suggested that PmAP2L was not a PETALOSA TOE-type gene,and it might be a new gene controlling the formation of double flower in P.mume.Subsequently,overexpression of PmAP2L-D in tobacco led to a significant rise in the number of stamens and the conversion of stamens to petals.Furthermore,silencing of the homologue of RC5G0530900 in rose significantly reduced the number of petals.Using transient gene expression in P.mume flower buds,we determined the functional differences between PmAP2L-D and PmAP2-S in controlling flower development.Meanwhile,DNA-affinity purification sequencing(DAP-seq),yeast hybrid assays and luciferase reporter assays indicated that PmAP2L negatively regulated the floral organ identity genes by forming a repressor complex with PmTPL and PmHDA6/19.Overall,these findings indicate that the variation in PmAP2L is associated with differences in the regulation of genes responsible for floral organ identity,providing new insights into the double-flower trait and double-flower breeding in plants.
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    Lskipk Lsatpase double mutants are necessary and sufficient for the compact plant architecture of butterhead lettuce

    Sai XieGuangbao LuoGuanghui AnBincai Wang...
    149-162页
    查看更多>>摘要：Lettuce,an important leafy vegetable crop worldwide,has rich variations in plant architecture.Butterhead lettuce,a popular horticul-tural type,has a unique plant architecture with loose leafy heads.The genetic and molecular mechanisms for such a compact plant architecture remain unclear.In this study we constructed a segregating population through crossing a butterhead cultivar and a stem lettuce cultivar.Genetic analysis identified the LsKIPK gene,which encodes a kinase,as the candidate gene controlling butterhead plant architecture.The Lskipk gene in the butterhead parent had a nonsense mutation,leading to a partial predicted protein.CRISPR/Cas9 and complementation tests verified its functions in plant architecture.We showed that the loss of function of LsKIPK is necessary but not sufficient for the butterhead plant architecture.To identify additional genes required for butterhead lettuce,we crossed a butterhead cultivar and a crisphead cultivar,both with the mutated Lskipk gene.Genetic mapping identified a new gene encoding an ATPase contributing to butterhead plant architecture.Knockout and complementation tests showed that loss of function of LsATPase is also required for the development of butterhead plant architecture.The Lskipk Lsatpase double mutation could reduce leaf size and leaf angle,leading to butterhead plant architecture.Expression and cytology analysis indicated that the loss of function of LsKIPK and LsATPase contributed to butterhead plant architecture by regulating cell wall development,a regulatory mechanism different from that for crisphead.This study provides new gene resources and theory for the breeding of the crop ideotype.
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    mRNA-miRNA analyses reveal the involvement of CsbHLH1 and miR1446a in the regulation of caffeine biosynthesis in Camellia sinensis

    Qifang JinZhong WangDevinder SandhuLan Chen...
    163-177页
    查看更多>>摘要：Caffeine,a primary flavor component in tea,has been the subject of intense research.With the goal of shedding light on the complex regulatory processes governing caffeine biosynthesis in tea plants,liquid chromatography coupled with mass spectrometry(LC-MS),transcriptomics,and small RNA analyses were employed on diverse tea cultivars such as'Jianghua Kucha'[including'Xianghong 3'(XH3H)and'Kucha 3'(KC3H)],'Fuding Dabaicha'(FDDB),'Yaoshan Xiulv'(YSXL),and'Bixiangzao'(BXZ).The results showed that the caffeine level in'Jianghua Kucha'was significantly higher than that in other tea plant cultivars.In addition,weighted gene co-expression network analysis indicated that that the CsbHLH1 gene might play a pivotal role as a potential hub gene related to the regulation of caffeine biosynthesis.Subcellular localization analysis showed that the CsbHLH1 protein was localized in the nucleus of the cells.Moreover,CsbHLH1 suppresses the transcription of TCS1 by binding to the TCS1 promoter,as evidenced by a yeast one-hybrid assay,an electrophoretic mobility shift assay,and dual luciferase analysis.In addition,a microRNA,miR1446a,was identified that directly cleaves CsbHLH1,leading to an increase in caffeine levels.Therefore,our findings imply that CsbHLH1 binds to the TCS1 promoter(-971 to-1019 bp)to reduce its expression,thereby negatively regulating caffeine biosynthesis.On the other hand,miR1446a enhances the biosynthesis of caffeine by suppressing the expression of CsbHLH1.This work enhances our understanding of the molecular mechanisms of caffeine biosynthesis in tea plants and offers potential directions for manipulating caffeine levels in future tea cultivation.
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    Dissecting the complex genetic basis of pre-and post-harvest traits in Vitis vinifera L.using genome-wide association studies

    Julian García-AbadilloPaola BarbaTiago CarvalhoViviana Sosa-Zu?iga...
    179-198页
    查看更多>>摘要：Addressing the pressing challenges in agriculture necessitates swift advancements in breeding programs,particularly for perennial crops like grapevines.Moving beyond the traditional biparental quantitative trait loci(QTL)mapping,we conducted a genome-wide association study(GWAS)encompassing 588 Vitis vinifera L.cultivars from a Chilean breeding program,spanning three seasons and testing 13 key yield-related traits.A strong candidate gene,Vitvi11g000454,located on chromosome 11 and related to plant response to biotic and abiotic stresses through jasmonic acid signaling,was associated with berry width and holds potential for enhancing berry size in grape breeding.We also mapped novel QTL associated with post-harvest traits across chromosomes 2,4,9,11,15,18,and 19,broadening our grasp on the genetic intricacies dictating fruit post-harvest behavior,including decay,shriveling,and weight loss.Leveraging gene ontology annotations,we drew parallels between traits and scrutinized candidate genes,laying a robust groundwork for future trait-feature identification endeavors in plant breeding.We also highlighted the importance of carefully considering the choice of the response variable in GWAS analyses,as the use of best linear unbiased estimators(BLUEs)corrections in our study may have led to the suppression of some common QTL in grapevine traits.Our results underscore the imperative of pioneering non-destructive evaluation techniques for long-term conservation traits,offering grape breeders and cultivators insights to improve post-harvest table grape quality and minimize waste.
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    Exploring N6-methyladenosine(m6A)modification in tree species:opportunities and challenges

    Muthusamy RamakrishnanK.Shanmugha RajanSileesh MullasseriZishan Ahmad...
    199-213页
    查看更多>>摘要：N6-methyladenosine(m6A)in eukaryotes is the most common and widespread internal modification in mRNA.The modification regulates mRNA stability,translation efficiency,and splicing,thereby fine-tuning gene regulation.In plants,m6A is dynamic and critical for various growth stages,embryonic development,morphogenesis,flowering,stress response,crop yield,and biomass.Although recent high-throughput sequencing approaches have enabled the rapid identification of m6A modification sites,the site-specific mechanism of this modification remains unclear in trees.In this review,we discuss the functional significance of m6A in trees under different stress conditions and discuss recent advancements in the quantification of m6A.Quantitative and functional insights into the dynamic aspect of m6 A modification could assist researchers in engineering tree crops for better productivity and resistance to various stress conditions.
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    AlliumDB:a central portal for comparative and functional genomics in Allium

    Pengtao YangYu YuanChao YanYue Jia...
    215-224页
    查看更多>>摘要：The genus Allium belongs to the botanical family Amaryllidaceae and includes economically important crops such as onion,garlic,bunching onion,and leek,used as vegetables,spices,and traditional medicines.The large sizes of Allium genomes hamper the genetic dissection of agronomically important traits and molecular breeding.With the growing accumulation of genomic,resequencing,transcriptome,and phenotypic data,the demand for an integrative Allium database is increasing.Here we present a user-friendly database,AlliumDB(https://allium.qau.edu.cn),as a functional genomics hub integrating public and in-house data.The database contains all currently available nuclear and organelle genomes for Allium species,with genes comprehensively annotated based on Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)analyses,orthology,gene families,protein families(Pfam),and non-coding RNA families(Rfam).Transcriptome and variation profiles are integrated into dynamic visualization tools.We took phenotypic photographs and generated trait records for hundreds of Allium germplasms collected worldwide,which are included in the database.We incorporated JBrowse for the visualization of gene structures,RNA sequencing data,and variation data.Analysis tools such as the basic local alignment search tool(BLAST),sequence fetch,enrichment,and motif analyses are available to explore potential gene functions.This database incorporates comprehensive Allium genotypic and phenotypic datasets.As the community assembles new genomes and generates resequencing data for Allium germplasms,the database will be improved and continuously updated with these multi-omics data and comparative genomic studies.We expect the AlliumDB database to become a key resource for the study of Allium crops.
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    NYUS.2:an automated machine learning prediction model for the large-scale real-time simulation of grapevine freezing tolerance in North America

    Hongrui WangGaurav D.MogheAl P.KovaleskiMarkus Keller...
    225-236页
    查看更多>>摘要：Accurate and real-time monitoring of grapevine freezing tolerance is crucial for the sustainability of the grape industry in cool climate viticultural regions.However,on-site data are limited due to the complexity of measurement.Current prediction models underperform under diverse climate conditions,which limits the large-scale deployment of these methods.We combined grapevine freezing tolerance data from multiple regions in North America and generated a predictive model based on hourly temperature-derived features and cultivar features using AutoGluon,an automated machine learning engine.Feature importance was quantified by AutoGluon and SHAP(SHapley Additive exPlanations)value.The final model was evaluated and compared with previous models for its performance under different climate conditions.The final model achieved an overall 1.36℃ root-mean-square error during model testing and outperformed two previous models using three test cultivars at all testing regions.Two feature importance quantification methods identified five shared essential features.Detailed analysis of the features indicates that the model has adequately extracted some biological mechanisms during training.The final model,named NYUS.2,was deployed along with two previous models as an R shiny-based application in the 2022-23 dormancy season,enabling large-scale and real-time simulation of grapevine freezing tolerance in North America for the first time.
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    IAA-miR164a-NAC100L1 module mediates symbiotic incompatibility of cucumber/pumpkin grafted seedlings through regulating callose deposition

    Mingzhu YuanTong JinJianqiang WuLan Li...
    237-250页
    查看更多>>摘要：Grafting is one of the key technologies to overcome the obstacles of continuous cropping,and improve crop yield and quality.However,the symbiotic incompatibility between rootstock and scion affects the normal growth and development of grafted seedlings after survival.The specific molecular regulation mechanism of graft incompatibility is still largely unclear.In this study,we found that the IAA-miR164a-NAC100L1 module induced callose deposition to mediate the symbiotic incompatibility of cucumber/pumpkin grafted seedlings.The incompatible combination(IG)grafting interface accumulated more callose,and the activity of callose synthase(CmCalS1)and IAA content were significantly higher than in the compatible combination(CG).Treatment with IAA polar transport inhibitor in the root of the IG plants decreased CmCalS activity and callose content.Furthermore,IAA negatively regulated the expression of Cm-miR164a,which directly targeted cleavage of CmNAC100L1.Interestingly,CmNAC100L1 interacted with CmCalS1 to regulate its activity.Further analysis showed that the interaction between CmNAC100L1 and CmCalS1 increased the activity of CmCalS1 in the IG plants but decreased it in the CG plants.Point mutation analysis revealed that threonine at the 57th position of CmCalS1 protein played a critical role to maintain its enzyme activity in the incompatible rootstock.Thus,IAA inhibited the expression of Cm-miR164a to elevate the expression of CmNAC100L1,which promoted CmNAC100L1 interaction with CmCalS1 to enhance CmCalS1 activity,resulting in callose deposition and symbiotic incompatibility of cucumber/pumpkin grafted seedlings.
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    MdSnRK1.1 interacts with MdGLK1 to regulate abscisic acid-mediated chlorophyll accumulation in apple

    Yu-Ying YangXiu-Hong AnLin RuiGuo-Dong Liu...
    251-264页
    查看更多>>摘要：Abscisic acid(ABA),as a plant hormone,plays a positive role in leaf chlorosis;however,the underlying molecular mechanism is less known.Our findings provide ABA treatment reduced the chlorophyll accumulation in apple,and Malus x domestica Sucrose Non-fermenting 1-Related Protein Kinase 1.1(MdSnRK1.1)participates in the process.MdSnRK1.1 interacts with MdGLK1,a GOLDEN2-like transcription factor that orchestrates development of the chloroplast.Furthermore,MdSnRK1.1 affects MdGLK1 protein stability through phosphorylation.We found that Ser468 of MdGLK1 is target site of MdSnRK1.1 phosphorylation.MdSnRK1.1-mediated phosphorylation was critical for MdGLK1 binding to the target gene MdHEMA1 promoters.Collectively,our results demonstrate that ABA activates MdSnRK1.1 to degrade MdGLK1 and inhibit the accumulation of chlorophyll.These findings extend our understanding on how MdSnRK1.1 balances normal growth and hormone response.
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    Transgressive segregation,hopeful monsters,and phenotypic selection drove rapid genetic gains and breakthroughs in predictive breeding for quantitative resistance to Macrophomina in strawberry

    Steven J.KnappGlenn S.ColeDominique D.A.PincotChristine Jade Dilla-Ermita...
    265-286页
    查看更多>>摘要：Two decades have passed since the strawberry(Fragaria × ananassa)disease caused by Macrophomina phaseolina,a necrotrophic soilborne fungal pathogen,began surfacing in California,Florida,and elsewhere.This disease has since become one of the most common causes of plant death and yield losses in strawberry.The Macrophomina problem emerged and expanded in the wake of the global phase-out of soil fumigation with methyl bromide and appears to have been aggravated by an increase in climate change-associated abiotic stresses.Here we show that sources of resistance to this pathogen are rare in gene banks and that the favorable alleles they carry are phenotypically unobvious.The latter were exposed by transgressive segregation and selection in populations phenotyped for resistance to Macrophomina under heat and drought stress.The genetic gains were immediate and dramatic.The frequency of highly resistant individuals increased from 1％in selection cycle 0 to 74％in selection cycle 2.Using GWAS and survival analysis,we found that phenotypic selection had increased the frequencies of favorable alleles among 10 loci associated with resistance and that favorable alleles had to be accumulated among four or more of these loci for an individual to acquire resistance.An unexpectedly straightforward solution to the Macrophomina disease resistance breeding problem emerged from our studies,which showed that highly resistant cultivars can be developed by genomic selection per se or marker-assisted stacking of favorable alleles among a comparatively small number of large-effect loci.
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