Low-temperature stresses limit the sustainability and productivity of grapevines when early spring frosts damage young grapevine leaves.Spring conditions often expose grapevines to low,but not damaging,chilling temper...Low-temperature stresses limit the sustainability and productivity of grapevines when early spring frosts damage young grapevine leaves.Spring conditions often expose grapevines to low,but not damaging,chilling temperatures and these temperatures have been shown to increase freeze resistance in other model systems.In this study,we examined whole-transcriptome gene expression patterns of young leaf tissue from cuttings of five different grapevine cultivars,exposed to chill and freeze shock,in order to understand the underlying transcriptional landscape associated with cold stress response.No visible damage was observed when grapevine leaves were exposed to chilling temperatures while freeze temperatures resulted in variable damage in all cultivars.Significant differences in gene expression were observed between warm control conditions and all types of cold stress.Exposure to chill stress(4°C)versus freezing stress(−3°C)resulted in very different patterns of gene expression and enriched pathway responses.Genes from the ethylene signaling,ABA signaling,the AP2/ERF,WRKY,and NAC transcription factor families,and starch/sucrose/galactose pathways were among the most commonly observed to be differentially regulated.Preconditioning leaves to chill temperatures prior to freezing temperatures resulted in slight buffering of gene expression responses,suggesting that differences between chill and freeze shock perception complicates identification of candidate genes for cold resistance in grapevine.Overall,the transcriptional landscape contrasts observed between low temperature and freezing stresses demonstrate very different activation of candidate pathways impacting grapevine cold response.展开更多
Vitis riparia,a critically important Native American grapevine species,is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxer...Vitis riparia,a critically important Native American grapevine species,is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxera epidemic.This species has abiotic and biotic stress tolerance and the largest natural geographic distribution of the North American grapevine species.Here we report an Illumina short-read 369X coverage,draft de novo heterozygous genome sequence of V.riparia Michx.‘Manitoba 37’with the size of~495 Mb for 69,616 scaffolds and a N50 length of 518,740 bp.Using RNAseq data,40,019 coding sequences were predicted and annotated.Benchmarking with Universal Single-Copy Orthologs(BUSCO)analysis of predicted gene models found 96%of the complete BUSCOs in this assembly.The assembly continuity and completeness were further validated using V.riparia ESTs,BACs,and three de novo transcriptome assemblies of three different V.riparia genotypes resulting in>98%of respective sequences/transcripts mapping with this assembly.Alignment of the V.riparia assembly and predicted CDS with the latest V.vinifera‘PN40024’CDS and genome assembly showed 99%CDS alignment and a high degree of synteny.An analysis of plant transcription factors indicates a high degree of homology with the V.vinifera transcription factors.QTL mapping to V.riparia‘Manitoba 37’and V.vinifera PN40024 has identified genetic relationships to phenotypic variation between species.This assembly provides reference sequences,gene models for marker development and understanding V.riparia’s genetic contributions in grape breeding and research.展开更多
‘Concord’,the most well-known juice grape with a parentage of the North American grape species Vitis labrusca L.,possesses a special‘foxy’aroma predominantly resulted from the accumulation of methyl anthranilate(M...‘Concord’,the most well-known juice grape with a parentage of the North American grape species Vitis labrusca L.,possesses a special‘foxy’aroma predominantly resulted from the accumulation of methyl anthranilate(MA)in berries.This aroma,however,is often perceived as an undesirable attribute by wine consumers and rarely noticeable in the common table and wine grape species V.vinifera.Here we discovered homology-induced promoter indels as a major genetic mechanism for species-specific regulation of a key‘foxy’aroma gene,anthraniloyl-CoA:methanol acyltransferase(AMAT),that is responsible for MA biosynthesis.We found the absence of a 426-bp and/or a 42-bp sequence in AMAT promoters highly associated with high levels of AMAT expression and MA accumulation in‘Concord’and other V.labrusca-derived grapes.These promoter variants,all with direct and inverted repeats,were further confirmed in more than 1,300 Vitis germplasm.Moreover,functional impact of these indels was validated in transgenic Arabidopsis.Superimposed on the promoter regulation,large structural changes including exonic insertion of a retrotransposon were present at the AMAT locus in some V.vinifera grapes.Elucidation of the AMAT genetic regulation advances our understanding of the‘foxy’aroma trait and makes it genetically trackable and amenable in grapevine breeding.展开更多
Marker-assisted selection(MAS)is often employed in crop breeding programs to accelerate and enhance cultivar development,via selection during the juvenile phase and parental selection prior to crossing.Next-generation...Marker-assisted selection(MAS)is often employed in crop breeding programs to accelerate and enhance cultivar development,via selection during the juvenile phase and parental selection prior to crossing.Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery.To bridge the gap between marker development and MAS implementation,this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery,low-cost genotyping through amplicon sequencing(AmpSeq)and decision making.The results document the development of a MAS package derived from genotyping-by-sequencing using three traits(flower sex,disease resistance and acylated anthocyanins)in grapevine breeding.The vast majority of sequence reads(⩾99%)were from the targeted regions.Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data,most amplicons(83 to 87%)had<10%missing data,and read depth had a median of 220–244×.Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy,flexibility,speed,high-throughput,low-cost and easily automated analysis.展开更多
Powdery mildew resistance genes restrict infection attempts at different stages of pathogenesis.Here,a strong and rapid powdery mildew resistance phenotype was discovered from Vitis amurensis‘PI 588631’that rapidly ...Powdery mildew resistance genes restrict infection attempts at different stages of pathogenesis.Here,a strong and rapid powdery mildew resistance phenotype was discovered from Vitis amurensis‘PI 588631’that rapidly stopped over 97%of Erysiphe necator conidia,before or immediately after emergence of a secondary hypha from appressoria.This resistance was effective across multiple years of vineyard evaluation on leaves,stems,rachises,and fruit and against a diverse array of E.necator laboratory isolates.Using core genome rhAmpSeq markers,resistance mapped to a single dominant locus(here named REN12)on chromosome 13 near 22.8–27.0 Mb,irrespective of tissue type,explaining up to 86.9%of the phenotypic variation observed on leaves.Shotgun sequencing of recombinant vines using skim-seq technology enabled the locus to be further resolved to a 780 kb region,from 25.15 to 25.93 Mb.RNASeq analysis indicated the allele-specific expression of four resistance genes(NLRs)from the resistant parent.REN12 is one of the strongest powdery mildew resistance loci in grapevine yet documented,and the rhAmpSeq sequences presented here can be directly used for marker-assisted selection or converted to other genotyping platforms.While no virulent isolates were identified among the genetically diverse isolates and wild populations of E.necator tested here,NLR loci like REN12 are often race-specific.Thus,stacking of multiple resistance genes and minimal use of fungicides should enhance the durability of resistance and could enable a 90%reduction in fungicides in low-rainfall climates where few other pathogens attack the foliage or fruit.展开更多
Abscisic acid(ABA)plays crucial regulatory roles in cold acclimation and deacclimation of grapevine,making it a potential tool to be utilized in vineyards for the acquisition of preferred phenotypes in winter and spri...Abscisic acid(ABA)plays crucial regulatory roles in cold acclimation and deacclimation of grapevine,making it a potential tool to be utilized in vineyards for the acquisition of preferred phenotypes in winter and spring.To understand the function of ABA,we conducted experiments during cold acclimation and deacclimation and evaluated the impact of exogenous ABA on the grapevine transcriptome.RNA-seq data were collected periodically hours or days after ABA treatment.Transcriptomic data were analyzed using principal component analysis(PCA),hierarchical clustering,unsupervised weighed gene co-expression network analysis(WGCNA),contrast-based differentially expressed genes(DEGs)identification and pre-ranked gene set enrichment analysis(GSEA).Our results suggest that ABA functions differently during cold acclimation and deacclimation by selectively regulating key pathways including auxin/indole acetic acid(IAA)metabolism,galactose metabolism and ribosome biogenesis.We also identified the activation of several apparent negative feedback systems that regulated ABA-induced transcriptomic changes,suggesting the existence of a balancing system in response to excessive ABA.This balancing systems potentially eliminates the long-term negative effect on grapevine growing from using ABA in the field.These findings advance our understanding about the regulation of grapevine physiology during dormancy and supports the potential of applying ABA as a cultural practice to mitigate cold injury in winter and spring.展开更多
The shoot structure of cultivated grapevine Vitis vinifera L.typically exhibits a three-node modular repetitive pattern,two sequential leaf-opposed tendrils followed by a tendril-free node.In this study,we investigate...The shoot structure of cultivated grapevine Vitis vinifera L.typically exhibits a three-node modular repetitive pattern,two sequential leaf-opposed tendrils followed by a tendril-free node.In this study,we investigated the molecular basis of this pattern by characterizing differentially expressed genes in 10 bulk samples of young tendril tissue from two grapevine populations showing segregation of mutant or wild-type shoot/tendril phyllotaxy.One population was the selfed progeny and the other one,an outcrossed progeny of a Vitis hybrid,‘Roger’s Red’.We analyzed 13375 expressed genes and carried out in-depth analyses of 324 of them,which were differentially expressed with a minimum of 1.5-fold changes between the mutant and wild-type bulk samples in both selfed and cross populations.A significant portion of these genes were direct cis-binding targets of 14 transcription factor families that were themselves differentially expressed.Network-based dependency analysis further revealed that most of the significantly rewired connections among the 10 most connected hub genes involved at least one transcription factor.TCP3 and MYB12,which were known important for plant-form development,were among these transcription factors.More importantly,TCP3 and MYB12 were found in this study to be involved in regulating the lignin gene PRX52,which is important to plant-form development.A further support evidence for the roles of TCP3-MYB12-PRX52 in contributing to tendril phyllotaxy was the findings of two other lignin-related genes uniquely expressed in the mutant phyllotaxy background.展开更多
FLOWERING LOCUS T(FT)can promote early flowering in annual species,but such role has not been well demonstrated in woody species.We produced self and reciprocal grafts involving non-transgenic blueberry(NT)and transge...FLOWERING LOCUS T(FT)can promote early flowering in annual species,but such role has not been well demonstrated in woody species.We produced self and reciprocal grafts involving non-transgenic blueberry(NT)and transgenic blueberry(T)carrying a 35S-driven blueberry FT(VcFT-OX).We demonstrated that the transgenic VcFT-OX rootstock promoted flowering of non-transgenic blueberry scions in the NT(scion):T(rootstock)grafts.We further analyzed RNASeq profiles and six groups of phytohormones in both NT:T and NT:NT plants.We observed content changes of several hormone metabolites,in a descending order,in the transgenic NT:T,non-transgenic NT:T,and non-transgenic NT:NT leaves.By comparing differential expression transcripts(DETs)of these tissues in relative to their control,we found that the non-transgenic NT:T leaves had many DETs shared with the transgenic NT:T leaves,but very few with the transgenic NT:T roots.Interestingly,a number of these shared DETs belong to hormone pathway genes,concurring with the content changes of hormone metabolites in both transgenic and non-transgenic leaves of the NT:T plants.These results suggest that phytohormones induced by VcFT-OX in the transgenic leaves might serve as part of the signals that resulted in early flowering in both transgenic plants and the non-transgenic NT:T scions.展开更多
The Dormancy-associated MADS-box(DAM)gene cluster in peach serves as a key regulatory hub on which the seasonal temperatures act and orchestrate dormancy onset and exit,chilling response and floral bud developmental p...The Dormancy-associated MADS-box(DAM)gene cluster in peach serves as a key regulatory hub on which the seasonal temperatures act and orchestrate dormancy onset and exit,chilling response and floral bud developmental pace.Yet,how different temperature regimes interact with and regulate the six linked DAM genes remains unclear.Here,we demonstrate that chilling downregulates DAM1 and DAM3–6 in dormant floral buds with distinct patterns and identify DAM4 as the most abundantly expressed one.We reveal multiple epigenetic events,with tri-methyl histone H3 lysine 27(H3K27me3)induced by chilling specifically in DAM1 and DAM5,a 21-nt sRNA in DAM3 and a ncRNA induced in DAM4.Such induction is inversely correlated with downregulation of their cognate DAMs.We also show that the six DAMs were hypermethylated,associating with the production of 24-nt sRNAs.Hence,the chilling-responsive dynamic of the different epigenetic elements and their interactions likely define distinct expression abundance and downregulation pattern of each DAM.We further show that the expression of the five DAMs remains steadily unchanged or continuously downregulated at the ensuing warm temperature after chilling,and this state of regulation correlates with robust increase of sRNA expression,H3K27me3 and CHH methylation,which is particularly pronounced in DAM4.Such robust increase of repressive epigenetic marks may irreversibly reinforce the chillingimposed repression of DAMs to ensure flower-developmental programming free from any residual DAM inhibition.Taken together,we reveal novel information about genetic and epigenetic regulation of the DAM cluster in peach,which will be of fundamental significance in understanding of the regulatory mechanisms underlying chilling requirement and dormancy release,and of practical application for improvement of plasticity of flower time and bud break in fruit trees to adapt changing climates.展开更多
The apple(Malus domestica)is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years.Here,we genetically characterise over 1000 ...The apple(Malus domestica)is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years.Here,we genetically characterise over 1000 apple accessions from the United States Department of Agriculture(USDA)germplasm collection using over 30,000 singlenucleotide polymorphisms(SNPs).We con fi rm the close genetic relationship between modern apple cultivars and their primary progenitor species,Malus sieversii from Central Asia,and fi nd that cider apples derive more of their ancestry from the European crabapple,Malus sylvestris,than do dessert apples.We determine that most of the USDA collection is a large complex pedigree:over half of the collection is interconnected by a series of fi rst-degree relationships.In addition,15%of the accessions have a fi rst-degree relationship with one of the top 8 cultivars produced in the USA.With the exception of‘Honeycrisp',the top 8 cultivars are interconnected to each other via pedigree relationships.The cultivars‘Golden Delicious'and‘Red Delicious'were found to have over 60 fi rst-degree relatives,consistent with their repeated use by apple breeders.We detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased fi rmness.Our results suggest that Americans are eating apples largely from a single family tree and that the apple's future improvement will bene fi t from increased exploitation of its tremendous natural genetic diversity.展开更多
The molecular mechanism underlying dormancy release and the induction of flowering remains poorly understood in woody plants.Mu-legacy is a valuable blueberry mutant,in which a transgene insertion caused increased exp...The molecular mechanism underlying dormancy release and the induction of flowering remains poorly understood in woody plants.Mu-legacy is a valuable blueberry mutant,in which a transgene insertion caused increased expression of a RESPONSE REGULATOR 2-like gene(VcRR2).Mu-legacy plants,compared with nontransgenic‘Legacy’plants,show dwarfing,promotion of flower bud formation,and can flower under nonchilling conditions.We conducted transcriptomic comparisons in leaves,chilled and nonchilled flowering buds,and late-pink buds,and analyzed a total of 41 metabolites of six groups of hormones in leaf tissues of both Mu-legacy and‘Legacy’plants.These analyses uncovered that increased VcRR2 expression promotes the expression of a homolog of Arabidopsis thaliana ENTCOPALYL DIPHOSPHATE SYNTHETASE 1(VcGA1),which induces new homeostasis of hormones,including increased gibberellin 4(GA4)levels in Mu-legacy leaves.Consequently,increased expression of VcRR2 and VcGA1,which function in cytokinin responses and gibberellin synthesis,respectively,initiated the reduction in plant height and the enhancement of flower bud formation of the Mu-legacy plants through interactions of multiple approaches.In nonchilled flower buds,29 differentially expressed transcripts of 17 genes of five groups of hormones were identified in transcriptome comparisons between Mu-legacy and‘Legacy’plants,of which 22 were chilling responsive.Thus,these analyses suggest that increased expression of VcRR2 was collectively responsible for promoting flower bud formation in highbush blueberry under nonchilling conditions.We report here for the first time the importance of VcRR2 to induce a suite of downstream hormones that promote flowering in woody plants.展开更多
Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural crops.Grafting is a common horticultural practice that...Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural crops.Grafting is a common horticultural practice that joins the roots(rootstock)of one plant to the shoot(scion)of another,providing an excellent method for investigating how these two organ systems affect each other.In this study,we used the French-American hybrid grapevine‘Chambourcin’(Vitis L.)as a model to explore the rootstock–scion relationship.We examined leaf shape,ion concentrations,and gene expression in‘Chambourcin’grown ungrafted as well as grafted to three different rootstocks(‘SO4’,‘1103P’and‘3309C’)across 2 years and three different irrigation treatments.We found that a significant amount of the variation in leaf shape could be explained by the interaction between rootstock and irrigation.For ion concentrations,the primary source of variation identified was the position of a leaf in a shoot,although rootstock and rootstock by irrigation interaction also explained a significant amount of variation for most ions.Lastly,we found rootstock-specific patterns of gene expression in grafted plants when compared to ungrafted vines.Thus,our work reveals the subtle and complex effect of grafting on‘Chambourcin’leaf morphology,ionomics,and gene expression.展开更多
Acidity and tannins are among the grape berry quality traits that influence wine quality.Despite advantageous environmental tolerances of Vitis aestivalis-derived‘Norton',its acidity and tannin concentrations oft...Acidity and tannins are among the grape berry quality traits that influence wine quality.Despite advantageous environmental tolerances of Vitis aestivalis-derived‘Norton',its acidity and tannin concentrations often deviate from expectations set for V.vinifera.Identification of the genetic determinants of malic acid,tartaric acid,pH,and tannin can assist in the improvement of new hybrid cultivars.For this purpose,a‘Norton'and V.vinifera‘Cabernet Sauvignon'hybrid population containing 223 individuals was used to construct a linkage map containing 384 simple sequence repeat(SSR)and 2,084 genotyping-by-sequencing(GBS)-derived single nucleotide polymorphism(SNP)markers.The resulting map was 1,441.9 cM in length with an average inter-marker distance of 0.75 cM and spanned 19 linkage groups(LGs).Quantitative trait loci(QTLs)were detected for malic acid,tartaric acid,pH,and tannin.QTLs for malic acid(LG 8)and pH(LG 6)were observed across multiple years and explained approximately 17.7%and 18.5%of the phenotypic variation,respectively.Additionally,QTLs for tartaric acid were identified on linkage groups 1,6,7,9,and 17 and tannin on LG 2 in single-year data.The QTLs for tartaric acid explained between 8.8−14.3%and tannin explained 24.7%of the phenotypic variation.The markers linked to these QTLs can be used to improve hybrid cultivar breeding through marker-assisted selection.展开更多
Powdery mildews present specific challenges to phenotyping systems that are based on imaging.Having previously developed lowthroughput,quantitative microscopy approaches for phenotyping resistance to Erysiphe necator ...Powdery mildews present specific challenges to phenotyping systems that are based on imaging.Having previously developed lowthroughput,quantitative microscopy approaches for phenotyping resistance to Erysiphe necator on thousands of grape leaf disk samples for genetic analysis,here we developed automated imaging and analysis methods for E.necator severity on leaf disks.By pairing a 46-megapixel CMOS sensor camera,a long-working distance lens providing 3.5×magnification,X-Y sample positioning,and Z-axis focusing movement,the system captured 78%of the area of a 1-cm diameter leaf disk in 3 to 10 focus-stacked images within 13.5 to 26 seconds.Each image pixel represented 1.44 m2 of the leaf disk.A convolutional neural network(CNN)based on GoogLeNet determined the presence or absence of E.necator hyphae in approximately 800 subimages per leaf disk as an assessment of severity,with a training validation accuracy of 94.3%.For an independent image set the CNN was in agreement with human experts for 89.3%to 91.7%of subimages.This live-imaging approach was nondestructive,and a repeated measures time course of infection showed differentiation among susceptible,moderate,and resistant samples.Processing over one thousand samples per day with good accuracy,the system can assess host resistance,chemical or biological efficacy,or other phenotypic responses of grapevine to E.necator.In addition,new CNNs could be readily developed for phenotyping within diverse pathosystems or for diverse traits amenable to leaf disk assays.展开更多
基金All research was supported by USDA appropriated funds for project number 1910-21220-006-00D.
文摘Low-temperature stresses limit the sustainability and productivity of grapevines when early spring frosts damage young grapevine leaves.Spring conditions often expose grapevines to low,but not damaging,chilling temperatures and these temperatures have been shown to increase freeze resistance in other model systems.In this study,we examined whole-transcriptome gene expression patterns of young leaf tissue from cuttings of five different grapevine cultivars,exposed to chill and freeze shock,in order to understand the underlying transcriptional landscape associated with cold stress response.No visible damage was observed when grapevine leaves were exposed to chilling temperatures while freeze temperatures resulted in variable damage in all cultivars.Significant differences in gene expression were observed between warm control conditions and all types of cold stress.Exposure to chill stress(4°C)versus freezing stress(−3°C)resulted in very different patterns of gene expression and enriched pathway responses.Genes from the ethylene signaling,ABA signaling,the AP2/ERF,WRKY,and NAC transcription factor families,and starch/sucrose/galactose pathways were among the most commonly observed to be differentially regulated.Preconditioning leaves to chill temperatures prior to freezing temperatures resulted in slight buffering of gene expression responses,suggesting that differences between chill and freeze shock perception complicates identification of candidate genes for cold resistance in grapevine.Overall,the transcriptional landscape contrasts observed between low temperature and freezing stresses demonstrate very different activation of candidate pathways impacting grapevine cold response.
基金supported by the National Science Foundation Award No.IIA1355423,USDA-NIFA SCRI Award No.2011–51181–30635 and the state of South Dakota.
文摘Vitis riparia,a critically important Native American grapevine species,is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxera epidemic.This species has abiotic and biotic stress tolerance and the largest natural geographic distribution of the North American grapevine species.Here we report an Illumina short-read 369X coverage,draft de novo heterozygous genome sequence of V.riparia Michx.‘Manitoba 37’with the size of~495 Mb for 69,616 scaffolds and a N50 length of 518,740 bp.Using RNAseq data,40,019 coding sequences were predicted and annotated.Benchmarking with Universal Single-Copy Orthologs(BUSCO)analysis of predicted gene models found 96%of the complete BUSCOs in this assembly.The assembly continuity and completeness were further validated using V.riparia ESTs,BACs,and three de novo transcriptome assemblies of three different V.riparia genotypes resulting in>98%of respective sequences/transcripts mapping with this assembly.Alignment of the V.riparia assembly and predicted CDS with the latest V.vinifera‘PN40024’CDS and genome assembly showed 99%CDS alignment and a high degree of synteny.An analysis of plant transcription factors indicates a high degree of homology with the V.vinifera transcription factors.QTL mapping to V.riparia‘Manitoba 37’and V.vinifera PN40024 has identified genetic relationships to phenotypic variation between species.This assembly provides reference sequences,gene models for marker development and understanding V.riparia’s genetic contributions in grape breeding and research.
基金supported by the USDA Agricultural Research Service.
文摘‘Concord’,the most well-known juice grape with a parentage of the North American grape species Vitis labrusca L.,possesses a special‘foxy’aroma predominantly resulted from the accumulation of methyl anthranilate(MA)in berries.This aroma,however,is often perceived as an undesirable attribute by wine consumers and rarely noticeable in the common table and wine grape species V.vinifera.Here we discovered homology-induced promoter indels as a major genetic mechanism for species-specific regulation of a key‘foxy’aroma gene,anthraniloyl-CoA:methanol acyltransferase(AMAT),that is responsible for MA biosynthesis.We found the absence of a 426-bp and/or a 42-bp sequence in AMAT promoters highly associated with high levels of AMAT expression and MA accumulation in‘Concord’and other V.labrusca-derived grapes.These promoter variants,all with direct and inverted repeats,were further confirmed in more than 1,300 Vitis germplasm.Moreover,functional impact of these indels was validated in transgenic Arabidopsis.Superimposed on the promoter regulation,large structural changes including exonic insertion of a retrotransposon were present at the AMAT locus in some V.vinifera grapes.Elucidation of the AMAT genetic regulation advances our understanding of the‘foxy’aroma trait and makes it genetically trackable and amenable in grapevine breeding.
基金The US Department of Agriculture National Institute of Food and Agriculture Specialty Crop Research Initiative provided funding for this project(award no.2011-51181-30635).
文摘Marker-assisted selection(MAS)is often employed in crop breeding programs to accelerate and enhance cultivar development,via selection during the juvenile phase and parental selection prior to crossing.Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery.To bridge the gap between marker development and MAS implementation,this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery,low-cost genotyping through amplicon sequencing(AmpSeq)and decision making.The results document the development of a MAS package derived from genotyping-by-sequencing using three traits(flower sex,disease resistance and acylated anthocyanins)in grapevine breeding.The vast majority of sequence reads(⩾99%)were from the targeted regions.Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data,most amplicons(83 to 87%)had<10%missing data,and read depth had a median of 220–244×.Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy,flexibility,speed,high-throughput,low-cost and easily automated analysis.
文摘Powdery mildew resistance genes restrict infection attempts at different stages of pathogenesis.Here,a strong and rapid powdery mildew resistance phenotype was discovered from Vitis amurensis‘PI 588631’that rapidly stopped over 97%of Erysiphe necator conidia,before or immediately after emergence of a secondary hypha from appressoria.This resistance was effective across multiple years of vineyard evaluation on leaves,stems,rachises,and fruit and against a diverse array of E.necator laboratory isolates.Using core genome rhAmpSeq markers,resistance mapped to a single dominant locus(here named REN12)on chromosome 13 near 22.8–27.0 Mb,irrespective of tissue type,explaining up to 86.9%of the phenotypic variation observed on leaves.Shotgun sequencing of recombinant vines using skim-seq technology enabled the locus to be further resolved to a 780 kb region,from 25.15 to 25.93 Mb.RNASeq analysis indicated the allele-specific expression of four resistance genes(NLRs)from the resistant parent.REN12 is one of the strongest powdery mildew resistance loci in grapevine yet documented,and the rhAmpSeq sequences presented here can be directly used for marker-assisted selection or converted to other genotyping platforms.While no virulent isolates were identified among the genetically diverse isolates and wild populations of E.necator tested here,NLR loci like REN12 are often race-specific.Thus,stacking of multiple resistance genes and minimal use of fungicides should enhance the durability of resistance and could enable a 90%reduction in fungicides in low-rainfall climates where few other pathogens attack the foliage or fruit.
基金This work was funded in part by the New York Grape and Wine Foundation,by U.S.Department of Agriculture appropriated project 1910-21220-006-00Dby The Ohio State University Research Competitive Grants Program(SEEDS)by The Ohio State University College of Food,Agricultural,and Environmental Sciences,Department of Horticulture and Crop Science。
文摘Abscisic acid(ABA)plays crucial regulatory roles in cold acclimation and deacclimation of grapevine,making it a potential tool to be utilized in vineyards for the acquisition of preferred phenotypes in winter and spring.To understand the function of ABA,we conducted experiments during cold acclimation and deacclimation and evaluated the impact of exogenous ABA on the grapevine transcriptome.RNA-seq data were collected periodically hours or days after ABA treatment.Transcriptomic data were analyzed using principal component analysis(PCA),hierarchical clustering,unsupervised weighed gene co-expression network analysis(WGCNA),contrast-based differentially expressed genes(DEGs)identification and pre-ranked gene set enrichment analysis(GSEA).Our results suggest that ABA functions differently during cold acclimation and deacclimation by selectively regulating key pathways including auxin/indole acetic acid(IAA)metabolism,galactose metabolism and ribosome biogenesis.We also identified the activation of several apparent negative feedback systems that regulated ABA-induced transcriptomic changes,suggesting the existence of a balancing system in response to excessive ABA.This balancing systems potentially eliminates the long-term negative effect on grapevine growing from using ABA in the field.These findings advance our understanding about the regulation of grapevine physiology during dormancy and supports the potential of applying ABA as a cultural practice to mitigate cold injury in winter and spring.
文摘The shoot structure of cultivated grapevine Vitis vinifera L.typically exhibits a three-node modular repetitive pattern,two sequential leaf-opposed tendrils followed by a tendril-free node.In this study,we investigated the molecular basis of this pattern by characterizing differentially expressed genes in 10 bulk samples of young tendril tissue from two grapevine populations showing segregation of mutant or wild-type shoot/tendril phyllotaxy.One population was the selfed progeny and the other one,an outcrossed progeny of a Vitis hybrid,‘Roger’s Red’.We analyzed 13375 expressed genes and carried out in-depth analyses of 324 of them,which were differentially expressed with a minimum of 1.5-fold changes between the mutant and wild-type bulk samples in both selfed and cross populations.A significant portion of these genes were direct cis-binding targets of 14 transcription factor families that were themselves differentially expressed.Network-based dependency analysis further revealed that most of the significantly rewired connections among the 10 most connected hub genes involved at least one transcription factor.TCP3 and MYB12,which were known important for plant-form development,were among these transcription factors.More importantly,TCP3 and MYB12 were found in this study to be involved in regulating the lignin gene PRX52,which is important to plant-form development.A further support evidence for the roles of TCP3-MYB12-PRX52 in contributing to tendril phyllotaxy was the findings of two other lignin-related genes uniquely expressed in the mutant phyllotaxy background.
文摘FLOWERING LOCUS T(FT)can promote early flowering in annual species,but such role has not been well demonstrated in woody species.We produced self and reciprocal grafts involving non-transgenic blueberry(NT)and transgenic blueberry(T)carrying a 35S-driven blueberry FT(VcFT-OX).We demonstrated that the transgenic VcFT-OX rootstock promoted flowering of non-transgenic blueberry scions in the NT(scion):T(rootstock)grafts.We further analyzed RNASeq profiles and six groups of phytohormones in both NT:T and NT:NT plants.We observed content changes of several hormone metabolites,in a descending order,in the transgenic NT:T,non-transgenic NT:T,and non-transgenic NT:NT leaves.By comparing differential expression transcripts(DETs)of these tissues in relative to their control,we found that the non-transgenic NT:T leaves had many DETs shared with the transgenic NT:T leaves,but very few with the transgenic NT:T roots.Interestingly,a number of these shared DETs belong to hormone pathway genes,concurring with the content changes of hormone metabolites in both transgenic and non-transgenic leaves of the NT:T plants.These results suggest that phytohormones induced by VcFT-OX in the transgenic leaves might serve as part of the signals that resulted in early flowering in both transgenic plants and the non-transgenic NT:T scions.
基金funded by the ARS-INHouse fund,USDA-NIFA grant(3200000379-16-182)the National Natural Science Foundation of China(31772371)and AoE grant(AoE/M-403/16).
文摘The Dormancy-associated MADS-box(DAM)gene cluster in peach serves as a key regulatory hub on which the seasonal temperatures act and orchestrate dormancy onset and exit,chilling response and floral bud developmental pace.Yet,how different temperature regimes interact with and regulate the six linked DAM genes remains unclear.Here,we demonstrate that chilling downregulates DAM1 and DAM3–6 in dormant floral buds with distinct patterns and identify DAM4 as the most abundantly expressed one.We reveal multiple epigenetic events,with tri-methyl histone H3 lysine 27(H3K27me3)induced by chilling specifically in DAM1 and DAM5,a 21-nt sRNA in DAM3 and a ncRNA induced in DAM4.Such induction is inversely correlated with downregulation of their cognate DAMs.We also show that the six DAMs were hypermethylated,associating with the production of 24-nt sRNAs.Hence,the chilling-responsive dynamic of the different epigenetic elements and their interactions likely define distinct expression abundance and downregulation pattern of each DAM.We further show that the expression of the five DAMs remains steadily unchanged or continuously downregulated at the ensuing warm temperature after chilling,and this state of regulation correlates with robust increase of sRNA expression,H3K27me3 and CHH methylation,which is particularly pronounced in DAM4.Such robust increase of repressive epigenetic marks may irreversibly reinforce the chillingimposed repression of DAMs to ensure flower-developmental programming free from any residual DAM inhibition.Taken together,we reveal novel information about genetic and epigenetic regulation of the DAM cluster in peach,which will be of fundamental significance in understanding of the regulatory mechanisms underlying chilling requirement and dormancy release,and of practical application for improvement of plasticity of flower time and bud break in fruit trees to adapt changing climates.
基金funding from the National Sciences and Engineering Research Council of Canada and Canada Research Chairs programme(SM).
文摘The apple(Malus domestica)is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years.Here,we genetically characterise over 1000 apple accessions from the United States Department of Agriculture(USDA)germplasm collection using over 30,000 singlenucleotide polymorphisms(SNPs).We con fi rm the close genetic relationship between modern apple cultivars and their primary progenitor species,Malus sieversii from Central Asia,and fi nd that cider apples derive more of their ancestry from the European crabapple,Malus sylvestris,than do dessert apples.We determine that most of the USDA collection is a large complex pedigree:over half of the collection is interconnected by a series of fi rst-degree relationships.In addition,15%of the accessions have a fi rst-degree relationship with one of the top 8 cultivars produced in the USA.With the exception of‘Honeycrisp',the top 8 cultivars are interconnected to each other via pedigree relationships.The cultivars‘Golden Delicious'and‘Red Delicious'were found to have over 60 fi rst-degree relatives,consistent with their repeated use by apple breeders.We detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased fi rmness.Our results suggest that Americans are eating apples largely from a single family tree and that the apple's future improvement will bene fi t from increased exploitation of its tremendous natural genetic diversity.
基金supported by AgBioResearch of Michigan State University(http://www.canr.msu.edu/research/agbioresearch/)and USDA-NIFA AFRI 1015241 to P.P.E.and G.S.
文摘The molecular mechanism underlying dormancy release and the induction of flowering remains poorly understood in woody plants.Mu-legacy is a valuable blueberry mutant,in which a transgene insertion caused increased expression of a RESPONSE REGULATOR 2-like gene(VcRR2).Mu-legacy plants,compared with nontransgenic‘Legacy’plants,show dwarfing,promotion of flower bud formation,and can flower under nonchilling conditions.We conducted transcriptomic comparisons in leaves,chilled and nonchilled flowering buds,and late-pink buds,and analyzed a total of 41 metabolites of six groups of hormones in leaf tissues of both Mu-legacy and‘Legacy’plants.These analyses uncovered that increased VcRR2 expression promotes the expression of a homolog of Arabidopsis thaliana ENTCOPALYL DIPHOSPHATE SYNTHETASE 1(VcGA1),which induces new homeostasis of hormones,including increased gibberellin 4(GA4)levels in Mu-legacy leaves.Consequently,increased expression of VcRR2 and VcGA1,which function in cytokinin responses and gibberellin synthesis,respectively,initiated the reduction in plant height and the enhancement of flower bud formation of the Mu-legacy plants through interactions of multiple approaches.In nonchilled flower buds,29 differentially expressed transcripts of 17 genes of five groups of hormones were identified in transcriptome comparisons between Mu-legacy and‘Legacy’plants,of which 22 were chilling responsive.Thus,these analyses suggest that increased expression of VcRR2 was collectively responsible for promoting flower bud formation in highbush blueberry under nonchilling conditions.We report here for the first time the importance of VcRR2 to induce a suite of downstream hormones that promote flowering in woody plants.
基金supported by appropriated funds to USDAARS-GGRU for project 8060-21220-006-00Dsupported by the USDA National Institute of Food and Agriculture,and by Michigan State University AgBioResearchsupport from National Science Foundation(NSF)Plant Genome Research Program award DBI#154689,NSF/EPSCoR Cooperative Agreement#IIA-1355423 and BioSNTR which is funded in part by the South Dakota Research and Innovation Center that supported this research.
文摘Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural crops.Grafting is a common horticultural practice that joins the roots(rootstock)of one plant to the shoot(scion)of another,providing an excellent method for investigating how these two organ systems affect each other.In this study,we used the French-American hybrid grapevine‘Chambourcin’(Vitis L.)as a model to explore the rootstock–scion relationship.We examined leaf shape,ion concentrations,and gene expression in‘Chambourcin’grown ungrafted as well as grafted to three different rootstocks(‘SO4’,‘1103P’and‘3309C’)across 2 years and three different irrigation treatments.We found that a significant amount of the variation in leaf shape could be explained by the interaction between rootstock and irrigation.For ion concentrations,the primary source of variation identified was the position of a leaf in a shoot,although rootstock and rootstock by irrigation interaction also explained a significant amount of variation for most ions.Lastly,we found rootstock-specific patterns of gene expression in grafted plants when compared to ungrafted vines.Thus,our work reveals the subtle and complex effect of grafting on‘Chambourcin’leaf morphology,ionomics,and gene expression.
基金supported by Capacity Building Grants for Non-Land Grant College of Agriculture,Award No.2016-70001-24623Specialty Crop Research Initiative Competitive Grant,Award No.2017-51181-26829,from the USDA National Institute of Food and Agriculture.
文摘Acidity and tannins are among the grape berry quality traits that influence wine quality.Despite advantageous environmental tolerances of Vitis aestivalis-derived‘Norton',its acidity and tannin concentrations often deviate from expectations set for V.vinifera.Identification of the genetic determinants of malic acid,tartaric acid,pH,and tannin can assist in the improvement of new hybrid cultivars.For this purpose,a‘Norton'and V.vinifera‘Cabernet Sauvignon'hybrid population containing 223 individuals was used to construct a linkage map containing 384 simple sequence repeat(SSR)and 2,084 genotyping-by-sequencing(GBS)-derived single nucleotide polymorphism(SNP)markers.The resulting map was 1,441.9 cM in length with an average inter-marker distance of 0.75 cM and spanned 19 linkage groups(LGs).Quantitative trait loci(QTLs)were detected for malic acid,tartaric acid,pH,and tannin.QTLs for malic acid(LG 8)and pH(LG 6)were observed across multiple years and explained approximately 17.7%and 18.5%of the phenotypic variation,respectively.Additionally,QTLs for tartaric acid were identified on linkage groups 1,6,7,9,and 17 and tannin on LG 2 in single-year data.The QTLs for tartaric acid explained between 8.8−14.3%and tannin explained 24.7%of the phenotypic variation.The markers linked to these QTLs can be used to improve hybrid cultivar breeding through marker-assisted selection.
基金The US Department of Agriculture,National Institute of Foodand Agriculture,Specialty Crop Research Initiative provided funding for this project[awards 2011-51181-30635 and 2017-51181-26829].
文摘Powdery mildews present specific challenges to phenotyping systems that are based on imaging.Having previously developed lowthroughput,quantitative microscopy approaches for phenotyping resistance to Erysiphe necator on thousands of grape leaf disk samples for genetic analysis,here we developed automated imaging and analysis methods for E.necator severity on leaf disks.By pairing a 46-megapixel CMOS sensor camera,a long-working distance lens providing 3.5×magnification,X-Y sample positioning,and Z-axis focusing movement,the system captured 78%of the area of a 1-cm diameter leaf disk in 3 to 10 focus-stacked images within 13.5 to 26 seconds.Each image pixel represented 1.44 m2 of the leaf disk.A convolutional neural network(CNN)based on GoogLeNet determined the presence or absence of E.necator hyphae in approximately 800 subimages per leaf disk as an assessment of severity,with a training validation accuracy of 94.3%.For an independent image set the CNN was in agreement with human experts for 89.3%to 91.7%of subimages.This live-imaging approach was nondestructive,and a repeated measures time course of infection showed differentiation among susceptible,moderate,and resistant samples.Processing over one thousand samples per day with good accuracy,the system can assess host resistance,chemical or biological efficacy,or other phenotypic responses of grapevine to E.necator.In addition,new CNNs could be readily developed for phenotyping within diverse pathosystems or for diverse traits amenable to leaf disk assays.
