查看更多>>摘要：Avocado(Persea americana Mill.)is an economically valuable plant because of the high fatty acid content and unique flavor of its fruits.Its fatty acid content,especially the relatively high unsaturated fatty acid content,provides significant health benefits.We herein present a telomere-to-telomere gapless genome assembly(841.6 Mb)of West Indian avocado.The genome contains 40629 predicted protei-coding genes.Repeat sequences account for 57.9％of the genome.Notably,all telomeres,centromeres,and a nucleolar organizing region are included in this genome.Fragments from these three regions were observed via fluorescence in situ hybridization.We identified 376 potential disease resistance-related nucleotide-binding leucine-rich repeat genes.These genes,which are typically clustered on chromosomes,may be derived from gene duplication events.Five NLR genes(Pa11g0262,Pa02g4855,Pa07g3139,Pa07g0383,and Pa02g3196)were highly expressed in leaves,stems,and fruits,indicating they may be involved in avocado disease responses in multiple tissues.We also identified 128 genes associated with fatty acid biosynthesis and analyzed their expression patterns in leaves,stems,and fruits.Pa02g0113,which encodes one of 11 stearoyl-acyl carrier protein desaturases mediating C18 unsaturated fatty acid synthesis,was more highly expressed in the leaves than in the stems and fruits.These findings provide valuable insights that enhance our understanding of fatty acid biosynthesis in avocado.
查看更多>>摘要：Jojoba is an industrial oil crop planted in tropical arid areas,and its low-temperature sensitivity prevents its introduction into temperate areas.Studying the molecular mechanisms associated with cold acclimation in jojoba is advantageous for developing breeds with enhanced cold tolerance.In this study,metabolomic analysis revealed that various flavonols accumulate in jojoba during cold acclimation.Time-course transcriptomic analysis and weighted correlation network analysis(WGCNA)demonstrated that flavonol biosynthesis and jasmonates(JAs)signaling pathways played crucial roles in cold acclimation.Combining the biochemical and genetic analyses showed that ScMYB12 directly activated flavonol synthase gene(ScFLS).The interaction between ScMYB12 and transparent testa 8(ScTT8)promoted the expression of ScFLS,but the negative regulator ScJAZ13 in the JA signaling pathway interacted with ScTT8 to attenuate the transcriptional activity of the ScTT8 and ScMYB12 complex,leading to the downregulation of ScFLS.Cold acclimation stimulated the production of JA in jojoba leaves,promoted the degradation of ScJAZ13,and activated the transcriptional activity of ScTT8 and ScMYB12 complexes,leading to the accumulation of flavonols.Our findings reveal the molecular mechanism of JA-mediated flavonol biosynthesis during cold acclimation in jojoba and highlight the JA pathway as a promising means for enhancing cold tolerance in breeding efforts.
查看更多>>摘要：Centromeres in eukaryotes mediate the accurate segregation of chromosomes during cell division.They serve as essential functional units of chromosomes and play a core role in the process of genome evolution.Centromeres are composed of satellite repeats and highly repetitive centromeric retrotransposons(CRs),which vary greatly even among closely related species.Cucumber(Cucumis sativus)is a globally cultivated and economically important vegetable and the only species in the Cucumis genus with seven pairs of chromosomes.Therefore,studying the centromeres of the Cucumis subgenus may yield valuable insights into its genome structure and evolution.Using chromatin immunoprecipitation(ChIP)techniques,we isolated centromeric DNA from cucumber reference line 9930.Our investigation into cucumber centromeres uncovered the centromeric satellite sequence,designated as CentCs,and the prevalence of Ty1/Copia long terminal repeat retrotransposons.In addition,active genes were identified in the CsCENH3 nucleosome regions with low transcription levels.To the best of our knowledge,this is the first time that characterization of centromeres has been achieved in cucumber.Meanwhile,our results on the distribution of CentCs and CsCRs in the subgenus Cucumis indicate that the content of centromeric repeats in the wild variants was significantly reduced compared with the cultivated cucumber.The results provide evidence for centromeric DNA amplification that occurred during the domestication process from wild to cultivated cucumber.Furthermore,these findings may offer new information for enhancing our understanding of phylogenetic relationships in the Cucumis genus.
查看更多>>摘要：Long non-coding RNAs(lncRNAs)have gathered significant attention due to their pivotal role in plant growth,development,and biotic and abiotic stress resistance.Despite this,there is still little understanding regarding the functions of lncRNA in these domains in the tea plant(Camellia sinensis),mainly attributable to the insufficiencies in gene manipulation techniques for tea plants.In this study,we designed a novel strategy to identify evolutionarily conserved trans-lncRNA(ECT-lncRNA)pairs in plants.We used highly consistent base sequences in the exon-overlapping region between trans-lncRNAs and their target gene transcripts.Based on this method,we successfully screened 24 ECT-lncRNA pairs from at least two or more plant species.In tea,as observed in model plants such as Arabidopsis,alfalfa,potatoes,and rice,there exists a trans-lncRNA capable of forming an ECT-lncRNA pair with transcripts of the 12-oxophytodienoate reductase(OPR)family,denoted as the OPRL/OPR pair.Considering evolutionary perspectives,the OPRL gene cluster in each species likely originates from a replication event of the OPR gene cluster.Gene manipulation and gene expression analysis revealed that CsOPRL influences disease resistance by regulating CsOPR expression in tea plants.Furthermore,the knockout of StOPRL1 in Solanum tuberosum led to aberrant growth characteristics and strong resistance to fungal infection.This study provides insights into a strategy for the screening and functional verification of ECT-lncRNA pairs.
查看更多>>摘要：Potato is the third most important food crop,but cultivation is challenged by numerous diseases and adverse abiotic conditions.To combat diseases,frequent fungicide application is common.Knocking out susceptibility genes by genome editing could be a durable option to increase resistance.DMR6 has been described as a susceptibility gene in several crops,based on data that indicates increased resistance upon interruption of the gene function.In potato,Stdmr6-1 mutants have been described to have increased resistance against the late blight pathogen Phytophthora infestans in controlled conditions.Here,we present field evaluations of CRISPR/Cas9 mutants,in a location with a complex population of P.infestans,during four consecutive years that indicate increased resistance to late blight without any trade-off in terms of yield penalty or tuber quality.Furthermore,studies of potato tubers from the field trials indicated increased resistance to common scab,and the mutant lines exhibit increased resistance to early blight pathogen Alternaria solani in controlled conditions.Early blight and common scab are problematic targets in potato resistance breeding,as resistance genes are very scarce.The described broad-spectrum resistance of Stdmr6-1 mutants may further extend to some abiotic stress conditions.In controlled experiments of either drought simulation or salinity,Stdmr6-1 mutant plants are less affected than the background cultivar.Together,these results demonstrate the prospect of the Stdmr6-1 mutants as a useful tool in future sustainable potato cultivation without any apparent trade-offs.
Mai F.MinamikawaMiyuki KunihisaShigeki MoriyaTokurou Shimizu...
67-79页
查看更多>>摘要：With advances in next-generation sequencing technologies,various marker genotyping systems have been developed for genomics-based approaches such as genomic selection(GS)and genome-wide association study(GWAS).As new genotyping platforms are developed,data from different genotyping platforms must be combined.However,the potential use of combined data for GS and GWAS has not yet been clarified.In this study,the accuracy of genomic prediction(GP)and the detection power of GWAS increased for most fruit quality traits of apples when using combined data from different genotyping systems,Illumina Infinium single-nucleotide polymorphism array and genotyping by random amplicon sequencing-direct(GRAS-Di)systems.In addition,the GP model,which considered the inbreeding effect,further improved the accuracy of the seven fruit traits.Runs of homozygosity(ROH)islands overlapped with the significantly associated regions detected by the GWAS for several fruit traits.Breeders may have exploited these regions to select promising apples by breeders,increasing homozygosity.These results suggest that combining genotypic data from different genotyping platforms benefits the GS and GWAS of fruit quality traits in apples.Information on inbreeding could be beneficial for improving the accuracy of GS for fruit traits of apples;however,further analysis is required to elucidate the relationship between the fruit traits and inbreeding depression(e.g.decreased vigor).
查看更多>>摘要：Seed development and yield depend on the transport and supply of sugar.However,an insufficient supply of nutrients from maternal tissues to embryos results in seed abortion and yield reduction in Camellia oleifera.In this study,we systematically examined the route and regulatory mechanisms of sugar import into developing C.oleifera seeds using a combination of histological observations,transcriptome profiling,and functional analysis.Labelling with the tracer carboxyfluorescein revealed a symplasmic route in the integument and an apoplasmic route for postphloem transport at the maternal-filial interface.Enzymatic activity and histological observation showed that at early stages[180-220 days after pollination(DAP)]of embryo differentiation,the high hexose/sucrose ratio was primarily mediated by acid invertases,and the micropylar endosperm/suspensor provides a channel for sugar import.Through Camellia genomic profiling,we identified three plasma membrane-localized proteins including CoSWEET1b,CoSWEET15,and CoSUT2 and one tonoplast-localized protein CoSWEET2a in seeds and verified their ability to transport various sugars via transformation in yeast mutants and calli.In situ hybridization and profiling of glycometabolism-related enzymes further demonstrated that CoSWEET15 functions as a micropylar endosperm-specific gene,together with the cell wall acid invertase CoCWIN9,to support early embryo development,while CoSWEET1b,CoSWEET2a,and CoSUT2 function at transfer cells and chalazal nucellus coupled with CoCWIN9 and CoCWIN11 responsible for sugar entry in bulk into the filial tissue.Collectively,our findings provide the first comprehensive evidence of the molecular regulation of sugar import into and within C.oleifera seeds and provide a new target for manipulating seed development.
查看更多>>摘要：Eggplant is one of the most important vegetables worldwide,with some varieties displaying prickles.These prickles,present on the leaves,stems,and fruit calyxes,posing challenges during cultivation,harvesting,and transportation,making them an undesirable agronomic trait.However,the genetic mechanisms underlying prickle morphogenesis in eggplant remain poorly understood,impeding genetic improvements.In this study,genetic analyses revealed that prickle morphogenesis is governed by a single dominant nuclear gene,termed PE(Prickly Eggplant).Subsequent bulk segregant RNA-sequencing(BSR-seq)and linkage analysis preliminarily mapped PE to chromosome 6.This locus was then fine mapped to a 9233 bp interval in a segregating population of 1109 plants,harboring only one candidate gene,SmLOG1,which encodes a LONELY GUY(LOG)-family cytokinin biosynthetic enzyme.Expression analyses via transcriptome and qRT-PCR demonstrate that SmLOG1 is predominantly expressed in immature prickles.CRISPR-Cas9 knockout experiments targeting SmLOG1 in prickly parental line'PI 381159'abolished prickles across all tissues,confirming its critical role in prickle morphogenesis.Sequence analysis of SmLOG1 pinpointed variations solely within the non-coding region.We developed a cleaved amplified polymorphic sequences(CAPS)marker from a distinct SNP located at-735-bp within the SmLOG1 promoter,finding significant association with prickle variation in 190 eggplant germplasms.These findings enhance our understanding of the molecular mechanisms governing prickle development in eggplant and facilitate the use of marker-assisted selection(MAS)for breeding prickleless cultivars.
Alhagie K.ChamAlison K.AdamsPhillip A.WadlMa del Carmen Ojeda-Zacarías...
108-118页
查看更多>>摘要：Plant-insect interactions are often influenced by host-or insect-associated metagenomic community members.The relative abundance of insects and the microbes that modulate their interactions were obtained from sweetpotato(Ipomoea batatas)leaf-associated metagenomes using quantitative reduced representation sequencing and strain/species-level profiling with the Qmatey software.Positive correlations were found between whitefly(Bemisia tabaci)and its endosymbionts(Candidatus Hamiltonella defensa,Candidatus Portiera aleyrodidarum,and Rickettsia spp.)and negative correlations with nitrogen-fixing bacteria that implicate nitric oxide in sweetpotato-whitefly interaction.Genome-wide associations using 252 975 dosage-based markers,and metagenomes as a covariate to reduce false positive rates,implicated ethylene and cell wall modification in sweetpotato-whitefly interaction.The predictive abilities(PA)for whitefly and Ocypus olens abundance were high in both populations(68％-69％and 33.3％-35.8％,respectively)and 69.9％for Frankliniella occidentalis.The metagBLUP(gBLUP)prediction model,which fits the background metagenome-based Cao dissimilarity matrix instead of the marker-based relationship matrix(G-matrix),revealed moderate PA(35.3％-49.1％)except for O.olens(3％-10.1％).A significant gain in PA after modeling the metagenome as a covariate(gGBLUP,≤11％)confirms quantification accuracy and that the metagenome modulates phenotypic expression and might account for the missing heritability problem.Significant gains in PA were also revealed after fitting allele dosage(≤17.4％)and dominance effects(≤4.6％).Pseudo-diploidized genotype data underperformed for dominance models.Including segregation-distorted loci(SDL)increased PA by 6％-17.1％,suggesting that traits associated with fitness cost might benefit from the inclusion of SDL.Our findings confirm the holobiont theory of host-metagenome co-evolution and underscore its potential for breeding within the context of G × G × E interactions.
查看更多>>摘要：Flavonoids constitute the main nutraceuticals in the leaves of tea plants(Camellia sinensis).To date,although it is known that drought stress can negatively impact the biosynthesis of flavonoids in tea leaves,the mechanism behind this phenomenon is unclear.Herein,we report a protein phosphorylation mechanism that negatively regulates the biosynthesis of flavonoids in tea leaves in drought conditions.Transcriptional analysis revealed the downregulation of gene expression of flavonoid biosynthesis and the upregulation of CsMPK4a encoding a mitogen-activated protein kinase in leaves.Luciferase complementation and yeast two-hybrid assays disclosed that CsMPK4a interacted with CsWD40.Phosphorylation assay in vitro,specific protein immunity,and analysis of protein mass spectrometry indicated that Ser-216,Thr-221,and Ser-253 of CsWD40 were potential phosphorylation sites of CsMPK4a.Besides,the protein immunity analysis uncovered an increased phosphorylation level of CsWD40 in tea leaves under drought conditions.Mutation of the three phosphorylation sites generated dephosphorylated CsWD403A and phosphorylated CsWD403D variants,which were introduced into the Arabidopsis ttg1 mutant.Metabolic analysis showed that the anthocyanin and proanthocyanidin content was lower in ttg1:CsWD403D transgenic plants than ttg1::CsWD403A transgenic and wild type plants.The transient overexpression of CsWD403D downregulated the anthocyanidin biosynthesis in tea leaves.The dual-fluorescein protein complementation experiment showed that CsWD403D did not interact with CsMYB5a and CsAN2,two key transcription factors of procyanidins and anthocyanidins biosynthesis in tea plant.These findings indicate that the phosphorylation of CsWD40 by CsMPK4a downregulates the flavonoid biosynthesis in tea plants in drought stresses.
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