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园艺研究(英文)
园艺研究(英文)
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    Haplotype-resolved genome and mapping of freezing tolerance in the wild potato Solanum commersonii

    Jianke DongJingwen LiYingtao ZuoJin Wang...
    1-13页
    查看更多>>摘要:Solanum commersonii(2n=2x=24,1EBN,Endosperm Balance Number),native to the southern regions of Brazil,Uruguay,and north-eastern Argentina,is the first wild potato germplasm collected by botanists and exhibits a remarkable array of traits related to disease resistance and stress tolerance.In this study,we present a high-quality haplotype-resolved genome of S.commersonii.The two identified haplotypes demonstrate chromosome sizes of 706.48 and 711.55 Mb,respectively,with corresponding chromosome anchoring rates of 94.2 and 96.9%.Additionally,the contig N50 lengths are documented at 50.87 and 45.16 Mb.The gene annotation outcomes indicate that the haplotypes encompasses a gene count of 39 799 and 40078,respectively.The genome contiguity,completeness,and accuracy assessments collectively indicate that the current assembly has produced a high-quality genome of S.commersonii.Evolutionary analysis revealed significant positive selection acting on certain disease resistance genes,stress response genes,and environmentally adaptive genes during the evolutionary process of S.commersonii.These genes may be related to the formation of diverse and superior germplasm resources in the wild potato species S.commersonii.Furthermore,we utilized a hybrid population of S.commersonii and S.verrucosum to conduct the mapping of potato freezing tolerance genes.By combining BSA-seq analysis with traditional QTL mapping,we successfully mapped the potato freezing tolerance genes to a specific region on Chr07,spanning 1.25 Mb,with a phenotypic contribution rate of 18.81%.In short,current research provides a haplotype-resolved reference genome of the diploid wild potato species S.commersonii and establishes a foundation for further cloning and unraveling the mechanisms underlying cold tolerance in potatoes.

    Dynamic temporal transcriptome analysis reveals grape VlMYB59-VlCKX4 regulatory module controls fruit set

    Qiaofang ShiXufei LiShengdi YangXiaochun Zhao...
    14-26页
    查看更多>>摘要:Fruit set is a key stage in determining yield potential and guaranteeing quality formation and regulation.N-(2-chloro-4-pyridyl)-N'-phenylurea(CPPU)has been widely applied in grape production,the most iconic of which is the promotion of grape fruit set.However,current studies still lack the molecular mechanism of CPPU-induced grape fruit set.Here,the dynamic,high-resolution stage-specific transcriptome profiles were generated based on two different treatments and five developmental periods during fruit set in'Kyoho'grape(Vitis vinifera L.× V.labrusca L.).Pairwise comparison and functional category analysis showed that phytohormone action cytokinin was significantly enriched during the CPPU-induced grape fruit set,but not the natural one.Value differentially expressed gene(VDEG)was a newly proposed analysis strategy for mining genes related to the grape fruit set.Notably,the cytokinin metabolic process was significantly enriched among up-regulated VDEGs.Of importance,a key VDEG VlCKX4 related to the cytokinin metabolic process was identified as related to the grape fruit set.Overexpression of VlCKX4 gene promoted the Arabidopsis plants that produce more and heavier siliques.The transcription factor VlMYB59 directly bound to the promoter of VlCKX4 and activated its expression.Moreover,overexpression of VlMYB59 gene also promoted the Arabidopsis fruit set.Overall,VlMYB59 responded to CPPU treatment and directly activated the expression of VlCKX4,thus promoting the fruit set.A regulatory pathway of the VlMYB59-VlCKX4 module in the fruit set was uncovered,which provides important insights into the molecular mechanisms of the fruit set and good genetic resources for high fruit set rate breeding.

    SlTrxh functions downstream of SlMYB86 and positively regulates nitrate stress tolerance via S-nitrosation in tomato seedling

    Senlin ZengXudong SunJiali ZhaiXixian Li...
    27-39页
    查看更多>>摘要:Nitric oxide(NO)is a redox-dependent signaling molecule that plays a crucial role in regulating a wide range of biological processes in plants.It functions by post-translationally modifying proteins,primarily through S-nitrosation.Thioredoxin(Trx),a small and ubiquitous protein with multifunctional properties,plays a pivotal role in the antioxidant defense system.However,the regulatory mechanism governing the response of tomato Trxh(SlTrxh)to excessive nitrate stress remains unknown.In this study,overexpression or silencing of SlTrxh in tomato led to increased or decreased nitrate stress tolerance,respectively.The overexpression of SlTrxh resulted in a reduction in levels of reactive oxygen species(ROS)and an increase in S-nitrosothiol(SNO)contents;conversely,silencing SlTrxh exhibited the opposite trend.The level of S-nitrosated SlTrxh was increased and decreased in SlTrxh overexpression and RNAi plants after nitrate treatment,respectively.SlTrxh was found to be susceptible to S-nitrosation both in vivo and in vitro,with Cysteine 54 potentially being the key site for S-nitrosation.Protein interaction assays revealed that SlTrxh physically interacts with SlGrx9,and this interaction is strengthened by S-nitrosation.Moreover,a combination of yeast one-hybrid(Y1H),electrophoretic mobility shift assay(EMSA),chromatin immunoprecipitation-quantitative PCR(ChIP-qPCR),and transient expression assays confirmed the direct binding of SlMYB86 to the SlTrxh promoter,thereby enhancing its expression.SlMYB86 is located in the nucleus and SlMYB86 overexpressed and knockout tomato lines showed enhanced and decreased nitrate stress tolerance,respectively.Our findings indicate that SlTrxh functions downstream of SlMYB86 and highlight the potential significance of S-nitrosation of SlTrxh in modulating its function under nitrate stress.

    The gap-free genome of Forsythia suspensa illuminates the intricate landscape of centromeres

    Jian CuiCongle ZhuLisha ShenCongyang Yi...
    41-52页
    查看更多>>摘要:Forsythia suspensa,commonly known as weeping forsythia,holds significance in traditional medicine and horticulture.Despite its ecological and cultural importance,the existing reference genome presents challenges with duplications and gaps,hindering in-depth genomic analyses.Here,we present a Telomere-to-Telomere(T2T)assembly of the F.suspensa genome,integrating Oxford Nanopore Technologies(ONT)ultra-long,Hi-C datasets,and high-fidelity(HiFi)sequencing data.The T2T reference genome(Fsus-CHAU)consists of 14 chromosomes,totaling 688.79 Mb,and encompasses 33 932 predicted protein-coding genes.Additionally,we characterize functional centromeres in the F.suspensa genome by developing a specific CENH3 antibody.We demonstrate that centromeric regions in F.suspensa exhibit a diverse array of satellites,showcasing distinctive types with unconventional lengths across various chromosomes.This discovery offers implications for the adaptability of CENH3 and the potential influence on centromere dynamics.Furthermore,after assessing the insertion time of full-length LTRs within centromeric regions,we found that they are older compared to those across the entire genome,contrasting with observations in other species where centromeric retrotransposons are typically young.We hypothesize that asexual reproduction may impact retrotransposon dynamics,influencing centromere evolution.In conclusion,our T2T assembly of the F.suspensa genome,accompanied by detailed genomic annotations and centromere analysis,significantly enhances F.suspensa potential as a subject of study in fields ranging from ecology and horticulture to traditional medicine.

    Siderophore interactions drive the ability of Pseudomonas spp.consortia to protect tomato against Ralstonia solanacearum

    Zhengying ShaoShaohua GuXiaoni ZhangJiao Xue...
    53-66页
    查看更多>>摘要:The soil-borne bacterial pathogen Ralstonia solanacearum causes significant losses in Solanaceae crop production worldwide,including tomato,potato,and eggplant.To efficiently prevent outbreaks,it is essential to understand the complex interactions between pathogens and the microbiome.One promising mechanism for enhancing microbiome functionality is siderophore-mediated competition,which is shaped by the low iron availability in the rhizosphere.This study explores the critical role of iron competition in determining microbiome functionality and its potential for designing high-performance microbiome engineering strategies.We investigated the impact of siderophore-mediated interactions on the efficacy of Pseudomonas spp.consortia in suppressing R.solanacearum,both in vitro and in vivo.Our findings show that siderophore production significantly enhances the inhibitory effects of Pseudomonas strains on pathogen growth,while other metabolites are less effective under iron-limited conditions.Moreover,siderophores play a crucial role in shaping interactions within the consortia,ultimately determining the level of protection against bacterial wilt disease.This study highlights the key role of siderophores in mediating consortium interactions and their impact on tomato health.Our results also emphasize the limited efficacy of other secondary metabolites in iron-limited environments,underscoring the importance of siderophore-mediated competition in maintaining tomato health and suppressing disease.

    Development of super-infective ternary vector systems for enhancing the Agrobacterium-mediated plant transformation and genome editing efficiency

    Jin-hee JeongEun-young JeonMin Ki HwangYoung Jong Song...
    67-81页
    查看更多>>摘要:Agrobacterium-mediated transformation remains a cornerstone of plant biology,fueling advancements in molecular genetics,new genomic techniques(NGTs),and the biotech industry.However,recalcitrant crops and technical hurdles persist as bottlenecks.The goal was to develop super-infective ternary vector systems that integrate a novel salicylic acid-degrading enzyme,GABA,and ethylene-degrading enzymes,targeting the transformation of crops by neutralizing plant defense system on Agrobacterium.Firstly,both the effect and activity of introducing enzymes were validated in EHA105,an important Agrobacterium strain.Our study demonstrates that all ternary vector(Tv)system variants significantly enhance reporter expression in transient assays with Nicotiana benthamiana and Cannabis sativa.Specifically,incorporating a constitutive virG mutation with novel enzyme combinations increased GFP and RUBY expression in C.sativa by>5-fold and 13-fold,respectively.The Tv system,combined with a geminivirus replicon,markedly boosted GUS gene expression in tomato,enhancing genome editing efficiency.Notably,compared to controls,Tv-VS demonstrated up to 18-fold and 4.5-fold increases in genome editing efficiency in C.sativa and tomato,respectively.Additionally,stable transformation rates in tomato and Arabidopsis improved significantly,with Tv-VS showing a remarkable 2.5-fold increase in transformation efficiency compared to control strains.The research marks notable progress in Agrobacterium-mediated plant transformation.The innovative ternary vectors overcome plant defense mechanisms,enabling genetic manipulation in previously challenging plant species.This development is anticipated to broaden the applications of plant genetic engineering,contributing to advancements in crop genome editing.

    Restorer of fertility like 30,encoding a mitochondrion-localized pentatricopeptide repeat protein,regulates wood formation in poplar

    Xiaokang FuZiwei YangLi GuoLianjia Luo...
    82-93页
    查看更多>>摘要:Nuclear-mitochondrial communication is crucial for plant growth,particularly in the context of cytoplasmic male sterility(CMS)repair mechanisms linked to mitochondrial genome mutations.The restorer of fertility-like(RFL)genes,known for their role in CMS restoration,remain largely unexplored in plant development.In this study,we focused on the evolutionary relationship of RFL family genes in poplar specifically within the dioecious Salicaceae plants.PtoRFL30 was identified to be preferentially expressed in stem vasculature,suggesting a distinct correlation with vascular cambium development.Transgenic poplar plants overexpressing PtoRFL30 exhibited a profound inhibition of vascular cambial activity and xylem development.Conversely,RNA interference-mediated knockdown of PtoRFL30 led to increased wood formation.Importantly,we revealed that PtoRFL30 plays a crucial role in maintaining mitochondrial functional homeostasis.Treatment with mitochondrial activity inhibitors delayed wood development in PtoRFL30-RNAi transgenic plants.Further investigations unveiled significant variations in auxin accumulation levels within vascular tissues of PtoRFL30-transgenic plants.Wood development anomalies resulting from PtoRFL30 overexpression and knockdown were rectified by NAA and NPA treatments,respectively.Our findings underscore the essential role of the PtoRFL30-mediated mitochondrion-auxin signaling module in wood formation,shedding light on the intricate nucleus-organelle communication during secondary vascular development.

    Single-cell RNA sequencing reveals a high-resolution cell atlas of petals in Prunus mume at different flowering development stages

    Yuhong GuoXiling ChentJinhong LiQi Wang...
    94-103页
    查看更多>>摘要:Prunus mume(mei),a traditional ornamental plant in China,is renowned for its fragrant flowers,primarily emitted by its petals.However,the cell types of mei petals and where floral volatile synthesis occurs are rarely reported.The study used single-cell RNA sequencing to characterize the gene expression landscape in petals of P.mume'Fenhong Zhusha'at budding stage(BS)and full-blooming stage(FS).Six major cell types of petals were identified:epidermal cells(ECs),parenchyma cells(PCs),xylem parenchyma cells,phloem parenchyma cells,xylem vessels and fibers,and sieve elements and companion cells complex.Cell-specific marker genes in each cell type were provided.Floral volatiles from mei petals were measured at four flowering development stages,and their emissions increased from BS to FS,and decreased at the withering stage.Fifty-eight differentially expressed genes(DEGs)in benzenoid/phenylpropanoid pathway were screened using bulk RNA-seq data.Twenty-eight DEGs expression increased from BS to FS,indicating that they might play roles in floral volatile synthesis in P.mume,among which PmBAHD3 would participate in benzyl acetate synthesis.ScRNA-seq data showed that 27 DEGs mentioned above were expressed variously in different cell types.In situ hybridization confirmed that PmPAL2,PmCAD1,PmBAHD3,5,and PmEGS1 involved in floral volatile synthesis in mei petals are mainly expressed in EC,PC,and most vascular tissues,consistent with scRNA-seq data.The result indicates that benzyl acetate and eugenol,the characteristic volatiles in mei,are mostly synthesized in these cell types.The first petal single-cell atlas was constructed,offering new insights into the molecular mechanism of floral volatile synthesis.

    Phospholipid production and signaling by a plant defense inducer against Podosphaera xanthii is genotype-dependent

    Theoni MargaritopoulouEirini BairaChristos AnagnostopoulosKaterina-Eleni Vichou...
    104-115页
    查看更多>>摘要:Biotrophic phytopathogenic fungi such as Podosphaera xanthii have evolved sophisticated mechanisms to adapt to various environments causing powdery mildews leading to substantial yield losses.Today,due to known adverse effects of pesticides,development of alternative control means is crucial and can be achieved by combining plant protection products with resistant genotypes.Using plant defense inducers,natural molecules that stimulate plant immune system mimicking pathogen attack is sustainable,but information about their mode of action in different hosts or host genotypes is extremely limited.Reynoutria sachalinensis extract,a known plant defense inducer,especially through the Salicylic acid pathway in Cucurbitaceae crops against P.xanthii,was employed to analyze the signaling cascade of defense activation.Here,we demonstrate that R.sachalinensis extract enhances phospholipid production and signaling in a Susceptible to P.xanthii courgette genotype,while limited response is observed in an Intermediate Resistance genotype due to genetic resistance.Functional enrichment and cluster analysis of the upregulated expressed genes revealed that inducer application promoted mainly lipid-and membrane-related pathways in the Susceptible genotype.On the contrary,the Intermediate Resistance genotype exhibited elevated broad spectrum defense pathways at control conditions,while inducer application did not promote any significant changes.This outcome was obvious and at the metabolite level.Main factor distinguishing the Intermediate Resistance form the Susceptible genotype was the epigenetic regulated increased expression of a G3P acyltransferase catalyzing phospholipid production.Our study provides evidence on phospholipid-based signaling after plant defense inducer treatment,and the selective role of plant's genetic background.

    Association analysis of BSA-seq,BSR-seq,and RNA-seq reveals key genes involved in purple leaf formation in a tea population(Camellia sinensis)

    Yueqi WangJi-Qiang JinRui ZhangMengdi He...
    116-127页
    查看更多>>摘要:Purple tea,rich in anthocyanins,has a variety of health benefits and is attracting global interest.However,the regulation mechanism of anthocyanin in purple tea populations has not been extensively studied.In this experiment,RNA-seq,BSA-seq,and BSR-seq were performed using 30 individuals with extreme colors(dark-purple and green)in an F1 population of'Zijuan'and'Jinxuan'.The results show that 459 genes were differentially expressed in purple and green leaves,among which genes involved in the anthocyanin synthesis and transport pathway,such as CHS,F3H,ANS,MYB75,GST,MATE,and ABCC,were highly expressed in purple leaves.Moreover,there were multiple SNP/InDel variation sites on chromosomes 2 and 14 of the tea plant,as identified by BSA-seq.The integrated analysis identified two highly expressed genes(CsANS and CsMYB75)with SNP/InDel site variations in the purple tea plants.By silencing leaves,we proved that CsMYB75 could positively regulate anthocyanin accumulation and expression of related structural genes in tea plants.A 181-bp InDel in the CsMYB75 promoter was also found to be co-segregating with leaf color.The results of this study provide a theoretical reference for the molecular mechanism of anthocyanin accumulation in purple tea plants and contribute to the creation of new tea cultivars with high anthocyanin content.