Patterns of starch hydrolysis in stem,equatorial,and calyx zones of‘Honeycrisp’and‘Empire’apples(Malus sylvestris(L.)Mill var.domestica(Borkh.)Mansf.)during maturation and ripening,and in‘Gala’apples in response...Patterns of starch hydrolysis in stem,equatorial,and calyx zones of‘Honeycrisp’and‘Empire’apples(Malus sylvestris(L.)Mill var.domestica(Borkh.)Mansf.)during maturation and ripening,and in‘Gala’apples in response to propylene or 1-methylcyclopropene(1-MCP)treatments after harvest,were studied.Differences in zonal starch concentrations were found for‘Empire’and‘Gala’fruits,but not for‘Honeycrisp’.During maturation and ripening of‘Empire’,the concentration of starch was highest in the calyx end and lowest in the stem region.</title>Differences in rates of starch hydrolysis among zones were not detected.‘Honeycrisp’and‘Empire’had the highest concentration of sorbitol in the calyx region,whereas it was highest in the stem-end region in‘Gala’.The distribution differences of glucose,fructose,and sucrose were similar in all three cultivars;higher fructose and glucose concentrations in the stem region,and higher sucrose concentrations in the calyx end of the fruit.Postharvest treatment of‘Gala’with propylene did not affect the internal ethylene concentration of the fruit but 1-MCP markedly inhibited it.Starch concentrations were highest in the calyx end but gradients of starch among zones were not changed by postharvest treatment.The rate of hydrolysis was slowed by 1-MCP treatment,but was unaffected by propylene.Postharvest treatments influenced sorbitol,glucose,and fructose concentrations.Patterns of starch concentration among the zones did not confirm differences in ripening,but reflected its uneven distribution throughout the fruit during development.Therefore,measured differences in zonal starch are most likely related to starch accumulation during fruit development,rather than differences in rates of starch degradation during ripening.展开更多
Phytohormone ethylene largely determines apple fruit shelf life and storability.Previous studies demonstrated that MdACS1 and MdACS3a,which encode 1-aminocyclopropane-1-carboxylic acid synthases(ACS),are crucial in ap...Phytohormone ethylene largely determines apple fruit shelf life and storability.Previous studies demonstrated that MdACS1 and MdACS3a,which encode 1-aminocyclopropane-1-carboxylic acid synthases(ACS),are crucial in apple fruit ethylene production.MdACS1 is well-known to be intimately involved in the climacteric ethylene burst in fruit ripening,while MdACS3a has been regarded a main regulator for ethylene production transition from system 1(during fruit development)to system 2(during fruit ripening).However,MdACS3a was also shown to have limited roles in initiating the ripening process lately.To better assess their roles,fruit ethylene production and softening were evaluated at five time points during a 20-day post-harvest period in 97 Malus accessions and in 34 progeny from 2 controlled crosses.Allelotyping was accomplished using an existing marker(ACS1)for MdACS1 and two markers(CAPS866 and CAPS870)developed here to specifically detect the two null alleles(ACS3a-G289V and Mdacs3a)of MdACS3a.In total,952 Malus accessions were allelotyped with the three markers.The major findings included:The effect of MdACS1 was significant on fruit ethylene production and softening while that of MdACS3a was less detectable;allele MdACS1–2 was significantly associated with low ethylene and slow softening;under the same background of the MdACS1 allelotypes,null allele Mdacs3a(not ACS3a-G289V)could confer a significant delay of ethylene peak;alleles MdACS1–2 and Mdacs3a(excluding ACS3a-G289V)were highly enriched in M.domestica and M.hybrid when compared with those in M.sieversii.These findings are of practical implications in developing apples of low and delayed ethylene profiles by utilizing the beneficial alleles MdACS1-2 and Mdacs3a.展开更多
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
The abundance of predatory phytoseiid mites,Typhlodromus pyri,important biological control agents of spider mite pests in numerous crops,is positively influenced by the density of leaf trichomes and tuft-form domatia ...The abundance of predatory phytoseiid mites,Typhlodromus pyri,important biological control agents of spider mite pests in numerous crops,is positively influenced by the density of leaf trichomes and tuft-form domatia in vein axils.Identification of the genetic regions controlling both trophic levels could facilitate the improvement of predatory mite habitat in breeding programs.The abundance of T.pyri and non-glandular trichomes was measured in a segregating F1 family derived from the cross of the complex Vitis hybrid,‘Horizon’,with Illinois 547-1(V.rupestris B38×V.cinerea B9),finding positive correlation among traits.High density genetic maps were used to localize one major quantitative trait locus(QTL)on chromosome 1 of Illinois 547-1 associated with both predatory mite abundance and leaf trichomes.This QTL explained 23%of the variation in phytoseiid abundance and similar amounts of variance in domatia rating(21%),domatia size(16%),leaf bristle density(37%in veins and 33%in blades),and leaf hair density(20%in veins and 15%in blades).Another nine QTL distributed among chromosomes 1,2,5,8,and 15 were associated solely with trichome density,and explained 7–17%of the phenotypic variation.Combined,our results provide evidence of the genetic architecture of non-glandular trichomes in Vitis,with a major locus influencing trichome densities,domatia size and predatory mite abundance.This information is relevant for breeding grapevines with a more favorable habitat for biological control agents.展开更多
Acidity is a critical component determining apple fruit quality.Previous studies reported two major acidity quantitative trait loci(QTLs)on linkage groups(LGs)16(Ma)and 8(Ma3),respectively,and their homozygous genotyp...Acidity is a critical component determining apple fruit quality.Previous studies reported two major acidity quantitative trait loci(QTLs)on linkage groups(LGs)16(Ma)and 8(Ma3),respectively,and their homozygous genotypes mama and ma3ma3 usually confer low titratable acidity(TA)(<3.0 mg ml^(−1))to apple fruit.However,apples of genotypes Ma-(MaMa and Mama)or Ma3-(Ma3Ma3 and Ma3ma3)frequently show an acidity range spanning both regular(TA 3.0–10.0 mg ml^(−1))and high(TA>10mgml^(−1))acidity levels.To date,the genetic control for high-acidity apples remains essentially unknown.In order to map QTLs associated with high acidity,two genomic DNA pools,one for high acidity and the other for regular acidity,were created in an interspecific F1 population Royal Gala(Malus domestica)×PI 613988(M.sieversii)of 191 fruit-bearing progenies.By Illumina paired-end sequencing of the high and regular acidity pools,1,261,640 single-nucleotide variants(SNVs)commonly present in both pools were detected.Using allele frequency directional difference and density(AFDDD)mapping approach,one region on chromosome 4 and another on chromosome 6 were identified to be putatively associated with high acidity,and were named Ma6 and Ma4,respectively.Trait association analysis of DNA markers independently developed from the Ma6 and Ma4 regions confirmed the mapping of Ma6 and Ma4.In the background of MaMa,20.6%of acidity variation could be explained by Ma6,28.5%by Ma4,and 50.7%by the combination of both.The effects of Ma6 and Ma4 in the background of Mama were also significant,but lower.These findings provide important genetic insight into high acidity in apple.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
Brassica oleracea forms a diverse and economically significant crop group.Improvement efforts are often hindered by limited knowledge of diversity contained within available germplasm.Here,we employ genotyping-by-sequ...Brassica oleracea forms a diverse and economically significant crop group.Improvement efforts are often hindered by limited knowledge of diversity contained within available germplasm.Here,we employ genotyping-by-sequencing to investigate a diverse panel of 85 landrace and improved B.oleracea broccoli,cauliflower,and Chinese kale entries.Ultimately,21,680 high-quality SNPs were used to reveal a complex and admixed population structure and clarify phylogenetic relationships among B.oleracea groups.Each broccoli landrace contained,on average,8.4 times as many unique alleles as an improved broccoli and landraces collectively represented 81%of all broccoli-specific alleles.Commercial broccoli hybrids were largely represented by a single subpopulation identified within a complex population structure.Greater allelic diversity in landrace broccoli and 96.1%of SNPs differentiating improved cauliflower from landrace cauliflower were common to the larger pool of broccoli germplasm,supporting a parallel or later development of cauliflower due to introgression events from broccoli.Chinese kale was readily distinguished by principal coordinate analysis.Genotyping was accomplished with and without reliance upon a reference genome producing 141,317 and 20,815 filtered SNPs,respectively,supporting robust SNP discovery methods in neglected or unimproved crop groups that lack a reference genome.This work clarifies the population structure,phylogeny,and domestication footprints of landrace and improved B.oleracea broccoli using many genotyping-by-sequencing markers.Additionally,a large pool of genetic diversity contained in broccoli landraces is described which may enhance future breeding efforts.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
Viticulture,like other fields of agriculture,is currently facing important challenges that will be addressed only through sustained,dedicated and coordinated research.Although the methods used in biology have evolved ...Viticulture,like other fields of agriculture,is currently facing important challenges that will be addressed only through sustained,dedicated and coordinated research.Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature,in many domains of study,including grapevine research,there is a need to improve the findability,accessibility,interoperability and reusability(FAIR-ness)of these data.Considering the heterogeneous nature of the data produced,the transnational nature of the scientific community and the experience gained elsewhere,we have formed an open working group,in the framework of the International Grapevine Genome Program(www.vitaceae.org),to construct a coordinated federation of information systems holding grapevine data distributed around the world,providing an integrated set of interfaces supporting advanced data modeling,rich semantic integration and the next generation of data mining tools.To achieve this goal,it will be critical to develop,implement and adopt appropriate standards for data annotation and formatting.The development of this system,the GrapeIS,linking genotypes to phenotypes,and scientific research to agronomical and oeneological data,should provide new insights into grape biology,and allow the development of new varieties to meet the challenges of biotic and abiotic stress,environmental change,and consumer demand.展开更多
In the decades since the first cannabinoids were identified by scientists,research has focused almost exclusively on the function and capacity of cannabinoids asmedicines and intoxicants for humans and other vertebrat...In the decades since the first cannabinoids were identified by scientists,research has focused almost exclusively on the function and capacity of cannabinoids asmedicines and intoxicants for humans and other vertebrates.Very little is knownabout the adaptive value of cannabinoid production,though several hypotheses have been proposed including protection from ultraviolet radiation,pathogens,and herbivores.To test the prediction that genotypeswith greater concentrations of cannabinoidswill have reduced herbivory,a segregating F2 population of Cannabis sativa was leveraged to conduct lab-and field-based bioassays investigating the function of cannabinoids in mediating interactions with chewing herbivores.In the field,foliar cannabinoid concentration was inversely correlated with chewing herbivore damage.On detached leaves,Trichoplusia ni larvae consumed less leaf area and grew less when feeding on leaves with greater concentrations of cannabinoids.Scanning electron and light microscopy were used to characterize variation in glandular trichome morphology.Cannabinoid-free genotypes had trichomes that appeared collapsed.To isolate cannabinoids from confounding factors,artificial insect diet was amended with cannabinoids in a range of physiologically relevant concentrations.Larvae grew less and had lower rates of survival as cannabinoid concentration increased.These results support the hypothesis that cannabinoids function in defense against chewing herbivores.展开更多
Sex dimorphism and gene expression were studied in developing catkins in 159 F 2 individuals from the bioenergy crop Salix purpurea,and potential mechanisms and pathways for regulating sex development were explored.Di...Sex dimorphism and gene expression were studied in developing catkins in 159 F 2 individuals from the bioenergy crop Salix purpurea,and potential mechanisms and pathways for regulating sex development were explored.Differential expression,eQTL,bisulfite sequencing,and network analysis were used to characterize sex dimorphism,detect candidate master regulator genes,and identify pathways through which the sex determination region(SDR)may mediate sex dimorphism.Eleven genes are presented as candidates for master regulators of sex,supported by gene expression and network analyses.These include genes putatively involved in hormone signaling,epigenetic modification,and regulation of transcription.eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region.Furthermore,data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways.These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus.This further demonstrates the dynamic nature of SDRs in plants,which involves a multitude of mechanisms of sex determination and a high rate of turnover.展开更多
Vacuum packaging(VAC)is a promising postharvest technology for removal of astringency in persimmons.VAC treatment increased the loss of astringency in‘Mopan’persimmon while maintaining firmness and sensory quality o...Vacuum packaging(VAC)is a promising postharvest technology for removal of astringency in persimmons.VAC treatment increased the loss of astringency in‘Mopan’persimmon while maintaining firmness and sensory quality over an 8-d storage period.Transcriptomic and metabolomic analyses were used to investigate the effects of VAC on the metabolism of the fruit.Downregulation of genes involved in the proanthocyanidin(PA)synthesis pathway,as well as transport-related genes such as glutathione S-transferases L3-like(GSTs L3-like)and ATP-binding cassette subfamily G member-like(ABCG),was associated with astringency in VAC-treated fruit.Increased acetaldehyde that would occur as a result of the upregulation of alcohol dehydrogenase(ADH)and pyruvate decarboxylase(PDC),would bind with PA and facilitate deastringency.Upregulation of ethylene-responsive factors(ERF22,ERF21,ERF18,ERF17,ERF12,and ERF10)in ethylene signal transduction may also contribute to the activation of ADH and PDC genes,which would further facilitate deastringency.Downregulation of genes related to cell wall dissociation was associated with slower fruit softening.Expression of reactive oxygen species scavenging-related genes was upregulated in VAC-treated fruit.Genes associated with abscisic acid biosynthesis and signal transduction pathways had different expression patterns,resulting in lower abscisic acid content and delayed fruit ripening under VAC conditions.A series of genes in the carotenoid synthesis pathway were inhibited by VAC.Metabolomic analyses revealed increased contents of flavor amino acids,which would enhance sweet and umami taste while reducing the levels of malic acid,tartaric acid(contributing to sourness),andʟ-arginine(associated with bitterness).展开更多
Plant phenotyping has been recognized as a bottleneck for improving the efficiency of breeding programs,understanding plantenvironment interactions,and managing agricultural systems.In the past five years,imaging appr...Plant phenotyping has been recognized as a bottleneck for improving the efficiency of breeding programs,understanding plantenvironment interactions,and managing agricultural systems.In the past five years,imaging approaches have shown great potential for high-throughput plant phenotyping,resulting in more attention paid to imaging-based plant phenotyping.With this increased amount of image data,it has become urgent to develop robust analytical tools that can extract phenotypic traits accurately and rapidly.The goal of this review is to provide a comprehensive overview of the latest studies using deep convolutional neural networks(CNNs)in plant phenotyping applications.We specifically review the use of various CNN architecture for plant stress evaluation,plant development,and postharvest quality assessment.We systematically organize the studies based on technical developments resulting from imaging classification,object detection,and image segmentation,thereby identifying state-of-the-art solutions for certain phenotyping applications.Finally,we provide several directions for future research in the use of CNN architecture for plant phenotyping purposes.展开更多
Fusing three-dimensional(3D)and multispectral(MS)imaging data holds promise for high-throughput and comprehensive plant phenotyping to decipher genome-to-phenome knowledge.Acquiring high-quality 3D MS point clouds(3DM...Fusing three-dimensional(3D)and multispectral(MS)imaging data holds promise for high-throughput and comprehensive plant phenotyping to decipher genome-to-phenome knowledge.Acquiring high-quality 3D MS point clouds(3DMPCs)of plants remains challenging because of poor 3D data quality and limited radiometric calibration methods for plants with a complex canopy structure.Here,we present a novel 3D spatial–spectral data fusion approach to collect high-quality 3DMPCs of plants by integrating the next-best-view planning for adaptive data acquisition and neural reference field(NeREF)for radiometric calibration.This approach was used to acquire 3DMPCs of perilla,tomato,and rapeseed plants with diverse plant architecture and leaf morphological features evaluated by the accuracy of chlorophyll content and equivalent water thickness(EWT)estimation.The results showed that the completeness of plant point clouds collected by this approach was improved by an average of 23.6%compared with the fixed viewpoints alone.The NeREF-based radiometric calibration with the hemispherical reference outperformed the conventional calibration method by reducing the root mean square error(RMSE)of 58.93%for extracted reflectance spectra.The RMSE for chlorophyll content and EWT predictions decreased by 21.25%and 14.13%using partial least squares regression with the generated 3DMPCs.Collectively,our study provides an effective and efficient way to collect high-quality 3DMPCs of plants under natural light conditions,which improves the accuracy and comprehensiveness of phenotyping plant morphological and physiological traits,and thus will facilitate plant biology and genetic studies as well as crop breeding.展开更多
Cytokinins(CKs)are a class of adenine-derived plant hormones that plays pervasive roles in plant growth and development including cell division,morphogenesis,lateral bud outgrowth,leaf expansion and senescence.CKs as ...Cytokinins(CKs)are a class of adenine-derived plant hormones that plays pervasive roles in plant growth and development including cell division,morphogenesis,lateral bud outgrowth,leaf expansion and senescence.CKs as a“fountain of youth”prolongs leaf longevity by inhibiting leaf senescence,and therefore must be catabolized for senescence to occur.AtNAP,a senescence-specific transcription factor has a key role in promoting leaf senescence.The role of AtNAP in regulating CK catabolism is unknown.Here we report the identification and characterization of AtNAP-AtCKX3(cytokinin oxidase 3)module by which CKs are catabolized during leaf senescence in Arabidopsis.Like AtNAP,AtCKX3 is highly upregulated during leaf senescence.When AtNAP is chemically induced AtCKX3 is co-induced;and when AtNAP is knocked out,the expression of AtCKX3 is abolished.AtNAP physically binds to the cis element of the AtCKX3 promoter to direct its expression as revealed by yeast one-hybrid assays and in planta experiments.Leaves of the atckx3 knockout lines have higher CK concentrations and a delayed senescence phenotype compared with those of WT.In contrast,leaves with inducible expression of AtCKX3 have lower CK concentrations and exhibit a precocious senescence phenotype compared with WT.This research reveals that AtNAP transcription factor˗AtCKX3 module regulates leaf senescence by connecting two antagonist plant hormones abscisic acid and CKs.展开更多
Ultrafiltration was investigated for its ability to alter the composition of hemp seed protein isolates(HSPI)and modify its functional properties.Hemp seeds that were germinated for 0,1,3,and 5 days underwent alkaline...Ultrafiltration was investigated for its ability to alter the composition of hemp seed protein isolates(HSPI)and modify its functional properties.Hemp seeds that were germinated for 0,1,3,and 5 days underwent alkaline extraction and protein isolation by isoelectric precipitation(IP)or ultrafiltration(UF).UF processing with a 100 nm membrane resulted in the loss of off-color pigments as well as vicilin proteins and small peptides~9 kDa,which changed the physicochemical properties and functionality of HSPI.We found that HSPIs from UF were lighter in color and higher in protein purity than isolates from IP,but lower in solubility.Germination paired with UF increased the water holding capacity by 2.3 times,from 1.06 to 2.46 g water/g isolate,while oil holding capacity was unaffected by germination and UF.UF resulted in protein isolates with decreased foaming capacity and increased gelation concentration compared to IP,but 5-day germinated HSPIs had statistically unchanged emulsifying activity indexes between the two processing methods.Germination and UF are thus presented as clean-label processing techniques to modify the composition and functionality of HSPIs.展开更多
基金F.C.D.was supported by a Department of Horticulture Graduate AssistantshipFunding for this research was provided by the NY Apple Research and Development Program and AgroFresh+1 种基金This work was also supported by the USDA National Institute of Food and Agriculture,Hatch project 2013-14-483Improving Quality and Reducing Losses in Specialty Fruit Crops through Storage Technologies(NE-1336).
文摘Patterns of starch hydrolysis in stem,equatorial,and calyx zones of‘Honeycrisp’and‘Empire’apples(Malus sylvestris(L.)Mill var.domestica(Borkh.)Mansf.)during maturation and ripening,and in‘Gala’apples in response to propylene or 1-methylcyclopropene(1-MCP)treatments after harvest,were studied.Differences in zonal starch concentrations were found for‘Empire’and‘Gala’fruits,but not for‘Honeycrisp’.During maturation and ripening of‘Empire’,the concentration of starch was highest in the calyx end and lowest in the stem region.</title>Differences in rates of starch hydrolysis among zones were not detected.‘Honeycrisp’and‘Empire’had the highest concentration of sorbitol in the calyx region,whereas it was highest in the stem-end region in‘Gala’.The distribution differences of glucose,fructose,and sucrose were similar in all three cultivars;higher fructose and glucose concentrations in the stem region,and higher sucrose concentrations in the calyx end of the fruit.Postharvest treatment of‘Gala’with propylene did not affect the internal ethylene concentration of the fruit but 1-MCP markedly inhibited it.Starch concentrations were highest in the calyx end but gradients of starch among zones were not changed by postharvest treatment.The rate of hydrolysis was slowed by 1-MCP treatment,but was unaffected by propylene.Postharvest treatments influenced sorbitol,glucose,and fructose concentrations.Patterns of starch concentration among the zones did not confirm differences in ripening,but reflected its uneven distribution throughout the fruit during development.Therefore,measured differences in zonal starch are most likely related to starch accumulation during fruit development,rather than differences in rates of starch degradation during ripening.
基金This work was financially supported in part by the National Plant Germplasm System(NPGS),Apple Crop Germplasm Committee(CGC),Federal Formula Funds,and College of Agriculture and Life Science,Cornell University.
文摘Phytohormone ethylene largely determines apple fruit shelf life and storability.Previous studies demonstrated that MdACS1 and MdACS3a,which encode 1-aminocyclopropane-1-carboxylic acid synthases(ACS),are crucial in apple fruit ethylene production.MdACS1 is well-known to be intimately involved in the climacteric ethylene burst in fruit ripening,while MdACS3a has been regarded a main regulator for ethylene production transition from system 1(during fruit development)to system 2(during fruit ripening).However,MdACS3a was also shown to have limited roles in initiating the ripening process lately.To better assess their roles,fruit ethylene production and softening were evaluated at five time points during a 20-day post-harvest period in 97 Malus accessions and in 34 progeny from 2 controlled crosses.Allelotyping was accomplished using an existing marker(ACS1)for MdACS1 and two markers(CAPS866 and CAPS870)developed here to specifically detect the two null alleles(ACS3a-G289V and Mdacs3a)of MdACS3a.In total,952 Malus accessions were allelotyped with the three markers.The major findings included:The effect of MdACS1 was significant on fruit ethylene production and softening while that of MdACS3a was less detectable;allele MdACS1–2 was significantly associated with low ethylene and slow softening;under the same background of the MdACS1 allelotypes,null allele Mdacs3a(not ACS3a-G289V)could confer a significant delay of ethylene peak;alleles MdACS1–2 and Mdacs3a(excluding ACS3a-G289V)were highly enriched in M.domestica and M.hybrid when compared with those in M.sieversii.These findings are of practical implications in developing apples of low and delayed ethylene profiles by utilizing the beneficial alleles MdACS1-2 and Mdacs3a.
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 Specialty Crop Research Initiative of the National Institute of Food and Agriculture,U.S.Department of Agriculture,under award number 2011-51181-30635 and National Research Initiative award number 2004-35302-14725.
文摘The abundance of predatory phytoseiid mites,Typhlodromus pyri,important biological control agents of spider mite pests in numerous crops,is positively influenced by the density of leaf trichomes and tuft-form domatia in vein axils.Identification of the genetic regions controlling both trophic levels could facilitate the improvement of predatory mite habitat in breeding programs.The abundance of T.pyri and non-glandular trichomes was measured in a segregating F1 family derived from the cross of the complex Vitis hybrid,‘Horizon’,with Illinois 547-1(V.rupestris B38×V.cinerea B9),finding positive correlation among traits.High density genetic maps were used to localize one major quantitative trait locus(QTL)on chromosome 1 of Illinois 547-1 associated with both predatory mite abundance and leaf trichomes.This QTL explained 23%of the variation in phytoseiid abundance and similar amounts of variance in domatia rating(21%),domatia size(16%),leaf bristle density(37%in veins and 33%in blades),and leaf hair density(20%in veins and 15%in blades).Another nine QTL distributed among chromosomes 1,2,5,8,and 15 were associated solely with trichome density,and explained 7–17%of the phenotypic variation.Combined,our results provide evidence of the genetic architecture of non-glandular trichomes in Vitis,with a major locus influencing trichome densities,domatia size and predatory mite abundance.This information is relevant for breeding grapevines with a more favorable habitat for biological control agents.
基金supported in part by the Agriculture and Food Research Initiative competitive grant no.2014-67013-21660,National Institute of Food and Agriculture,US Department of Agriculture(NIFA,USDA).
文摘Acidity is a critical component determining apple fruit quality.Previous studies reported two major acidity quantitative trait loci(QTLs)on linkage groups(LGs)16(Ma)and 8(Ma3),respectively,and their homozygous genotypes mama and ma3ma3 usually confer low titratable acidity(TA)(<3.0 mg ml^(−1))to apple fruit.However,apples of genotypes Ma-(MaMa and Mama)or Ma3-(Ma3Ma3 and Ma3ma3)frequently show an acidity range spanning both regular(TA 3.0–10.0 mg ml^(−1))and high(TA>10mgml^(−1))acidity levels.To date,the genetic control for high-acidity apples remains essentially unknown.In order to map QTLs associated with high acidity,two genomic DNA pools,one for high acidity and the other for regular acidity,were created in an interspecific F1 population Royal Gala(Malus domestica)×PI 613988(M.sieversii)of 191 fruit-bearing progenies.By Illumina paired-end sequencing of the high and regular acidity pools,1,261,640 single-nucleotide variants(SNVs)commonly present in both pools were detected.Using allele frequency directional difference and density(AFDDD)mapping approach,one region on chromosome 4 and another on chromosome 6 were identified to be putatively associated with high acidity,and were named Ma6 and Ma4,respectively.Trait association analysis of DNA markers independently developed from the Ma6 and Ma4 regions confirmed the mapping of Ma6 and Ma4.In the background of MaMa,20.6%of acidity variation could be explained by Ma6,28.5%by Ma4,and 50.7%by the combination of both.The effects of Ma6 and Ma4 in the background of Mama were also significant,but lower.These findings provide important genetic insight into high acidity in apple.
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.
基金This work is supported by Specialty Crop Research Initiative grant no.2016-51181-25402 from the USDA National Institute of Food and Agriculture.
文摘Brassica oleracea forms a diverse and economically significant crop group.Improvement efforts are often hindered by limited knowledge of diversity contained within available germplasm.Here,we employ genotyping-by-sequencing to investigate a diverse panel of 85 landrace and improved B.oleracea broccoli,cauliflower,and Chinese kale entries.Ultimately,21,680 high-quality SNPs were used to reveal a complex and admixed population structure and clarify phylogenetic relationships among B.oleracea groups.Each broccoli landrace contained,on average,8.4 times as many unique alleles as an improved broccoli and landraces collectively represented 81%of all broccoli-specific alleles.Commercial broccoli hybrids were largely represented by a single subpopulation identified within a complex population structure.Greater allelic diversity in landrace broccoli and 96.1%of SNPs differentiating improved cauliflower from landrace cauliflower were common to the larger pool of broccoli germplasm,supporting a parallel or later development of cauliflower due to introgression events from broccoli.Chinese kale was readily distinguished by principal coordinate analysis.Genotyping was accomplished with and without reliance upon a reference genome producing 141,317 and 20,815 filtered SNPs,respectively,supporting robust SNP discovery methods in neglected or unimproved crop groups that lack a reference genome.This work clarifies the population structure,phylogeny,and domestication footprints of landrace and improved B.oleracea broccoli using many genotyping-by-sequencing markers.Additionally,a large pool of genetic diversity contained in broccoli landraces is described which may enhance future breeding efforts.
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.
基金The foundations and the first draft of this paper were set up during a workshop organized in Bordeaux,France in February 2015 with the financial support of the Gallo Wine Company,INRA and of the Institut des Sciences de la Vigne et du Vin.
文摘Viticulture,like other fields of agriculture,is currently facing important challenges that will be addressed only through sustained,dedicated and coordinated research.Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature,in many domains of study,including grapevine research,there is a need to improve the findability,accessibility,interoperability and reusability(FAIR-ness)of these data.Considering the heterogeneous nature of the data produced,the transnational nature of the scientific community and the experience gained elsewhere,we have formed an open working group,in the framework of the International Grapevine Genome Program(www.vitaceae.org),to construct a coordinated federation of information systems holding grapevine data distributed around the world,providing an integrated set of interfaces supporting advanced data modeling,rich semantic integration and the next generation of data mining tools.To achieve this goal,it will be critical to develop,implement and adopt appropriate standards for data annotation and formatting.The development of this system,the GrapeIS,linking genotypes to phenotypes,and scientific research to agronomical and oeneological data,should provide new insights into grape biology,and allow the development of new varieties to meet the challenges of biotic and abiotic stress,environmental change,and consumer demand.
文摘In the decades since the first cannabinoids were identified by scientists,research has focused almost exclusively on the function and capacity of cannabinoids asmedicines and intoxicants for humans and other vertebrates.Very little is knownabout the adaptive value of cannabinoid production,though several hypotheses have been proposed including protection from ultraviolet radiation,pathogens,and herbivores.To test the prediction that genotypeswith greater concentrations of cannabinoidswill have reduced herbivory,a segregating F2 population of Cannabis sativa was leveraged to conduct lab-and field-based bioassays investigating the function of cannabinoids in mediating interactions with chewing herbivores.In the field,foliar cannabinoid concentration was inversely correlated with chewing herbivore damage.On detached leaves,Trichoplusia ni larvae consumed less leaf area and grew less when feeding on leaves with greater concentrations of cannabinoids.Scanning electron and light microscopy were used to characterize variation in glandular trichome morphology.Cannabinoid-free genotypes had trichomes that appeared collapsed.To isolate cannabinoids from confounding factors,artificial insect diet was amended with cannabinoids in a range of physiologically relevant concentrations.Larvae grew less and had lower rates of survival as cannabinoid concentration increased.These results support the hypothesis that cannabinoids function in defense against chewing herbivores.
基金Support for this research was provided by grants(DEB-1542486,DEB-1542599)from the National Science Foundationfrom the USDA National Institute for Food and Agriculture(2015-67009-23957)。
文摘Sex dimorphism and gene expression were studied in developing catkins in 159 F 2 individuals from the bioenergy crop Salix purpurea,and potential mechanisms and pathways for regulating sex development were explored.Differential expression,eQTL,bisulfite sequencing,and network analysis were used to characterize sex dimorphism,detect candidate master regulator genes,and identify pathways through which the sex determination region(SDR)may mediate sex dimorphism.Eleven genes are presented as candidates for master regulators of sex,supported by gene expression and network analyses.These include genes putatively involved in hormone signaling,epigenetic modification,and regulation of transcription.eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region.Furthermore,data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways.These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus.This further demonstrates the dynamic nature of SDRs in plants,which involves a multitude of mechanisms of sex determination and a high rate of turnover.
基金funded by the Special Innovation Ability Construction Fund of Beijing Academy of Agricultural and Forestry Sciences,China(KJCX20251211)the National Key Research and Development Program of China(No.2023YFD2201300).
文摘Vacuum packaging(VAC)is a promising postharvest technology for removal of astringency in persimmons.VAC treatment increased the loss of astringency in‘Mopan’persimmon while maintaining firmness and sensory quality over an 8-d storage period.Transcriptomic and metabolomic analyses were used to investigate the effects of VAC on the metabolism of the fruit.Downregulation of genes involved in the proanthocyanidin(PA)synthesis pathway,as well as transport-related genes such as glutathione S-transferases L3-like(GSTs L3-like)and ATP-binding cassette subfamily G member-like(ABCG),was associated with astringency in VAC-treated fruit.Increased acetaldehyde that would occur as a result of the upregulation of alcohol dehydrogenase(ADH)and pyruvate decarboxylase(PDC),would bind with PA and facilitate deastringency.Upregulation of ethylene-responsive factors(ERF22,ERF21,ERF18,ERF17,ERF12,and ERF10)in ethylene signal transduction may also contribute to the activation of ADH and PDC genes,which would further facilitate deastringency.Downregulation of genes related to cell wall dissociation was associated with slower fruit softening.Expression of reactive oxygen species scavenging-related genes was upregulated in VAC-treated fruit.Genes associated with abscisic acid biosynthesis and signal transduction pathways had different expression patterns,resulting in lower abscisic acid content and delayed fruit ripening under VAC conditions.A series of genes in the carotenoid synthesis pathway were inhibited by VAC.Metabolomic analyses revealed increased contents of flavor amino acids,which would enhance sweet and umami taste while reducing the levels of malic acid,tartaric acid(contributing to sourness),andʟ-arginine(associated with bitterness).
基金The project was supported by the National Robotics Initiative(NIFA grant no.2017-67021-25928).
文摘Plant phenotyping has been recognized as a bottleneck for improving the efficiency of breeding programs,understanding plantenvironment interactions,and managing agricultural systems.In the past five years,imaging approaches have shown great potential for high-throughput plant phenotyping,resulting in more attention paid to imaging-based plant phenotyping.With this increased amount of image data,it has become urgent to develop robust analytical tools that can extract phenotypic traits accurately and rapidly.The goal of this review is to provide a comprehensive overview of the latest studies using deep convolutional neural networks(CNNs)in plant phenotyping applications.We specifically review the use of various CNN architecture for plant stress evaluation,plant development,and postharvest quality assessment.We systematically organize the studies based on technical developments resulting from imaging classification,object detection,and image segmentation,thereby identifying state-of-the-art solutions for certain phenotyping applications.Finally,we provide several directions for future research in the use of CNN architecture for plant phenotyping purposes.
基金funded by the National Natural Science Foundation of China(32371985)the Fundamental Research Funds for the Central Universities,China(226-2022-00217).
文摘Fusing three-dimensional(3D)and multispectral(MS)imaging data holds promise for high-throughput and comprehensive plant phenotyping to decipher genome-to-phenome knowledge.Acquiring high-quality 3D MS point clouds(3DMPCs)of plants remains challenging because of poor 3D data quality and limited radiometric calibration methods for plants with a complex canopy structure.Here,we present a novel 3D spatial–spectral data fusion approach to collect high-quality 3DMPCs of plants by integrating the next-best-view planning for adaptive data acquisition and neural reference field(NeREF)for radiometric calibration.This approach was used to acquire 3DMPCs of perilla,tomato,and rapeseed plants with diverse plant architecture and leaf morphological features evaluated by the accuracy of chlorophyll content and equivalent water thickness(EWT)estimation.The results showed that the completeness of plant point clouds collected by this approach was improved by an average of 23.6%compared with the fixed viewpoints alone.The NeREF-based radiometric calibration with the hemispherical reference outperformed the conventional calibration method by reducing the root mean square error(RMSE)of 58.93%for extracted reflectance spectra.The RMSE for chlorophyll content and EWT predictions decreased by 21.25%and 14.13%using partial least squares regression with the generated 3DMPCs.Collectively,our study provides an effective and efficient way to collect high-quality 3DMPCs of plants under natural light conditions,which improves the accuracy and comprehensiveness of phenotyping plant morphological and physiological traits,and thus will facilitate plant biology and genetic studies as well as crop breeding.
基金The work was supported by Cornell University.Y.H.and B.L.were funded by scholarships from China Scholars Council.
文摘Cytokinins(CKs)are a class of adenine-derived plant hormones that plays pervasive roles in plant growth and development including cell division,morphogenesis,lateral bud outgrowth,leaf expansion and senescence.CKs as a“fountain of youth”prolongs leaf longevity by inhibiting leaf senescence,and therefore must be catabolized for senescence to occur.AtNAP,a senescence-specific transcription factor has a key role in promoting leaf senescence.The role of AtNAP in regulating CK catabolism is unknown.Here we report the identification and characterization of AtNAP-AtCKX3(cytokinin oxidase 3)module by which CKs are catabolized during leaf senescence in Arabidopsis.Like AtNAP,AtCKX3 is highly upregulated during leaf senescence.When AtNAP is chemically induced AtCKX3 is co-induced;and when AtNAP is knocked out,the expression of AtCKX3 is abolished.AtNAP physically binds to the cis element of the AtCKX3 promoter to direct its expression as revealed by yeast one-hybrid assays and in planta experiments.Leaves of the atckx3 knockout lines have higher CK concentrations and a delayed senescence phenotype compared with those of WT.In contrast,leaves with inducible expression of AtCKX3 have lower CK concentrations and exhibit a precocious senescence phenotype compared with WT.This research reveals that AtNAP transcription factor˗AtCKX3 module regulates leaf senescence by connecting two antagonist plant hormones abscisic acid and CKs.
基金funded by the Good Food Institute as well as the New York State Department of AgricultureMarkets with grants from the Empire State Development Corporation(AC477,AC483,and#132,997).
文摘Ultrafiltration was investigated for its ability to alter the composition of hemp seed protein isolates(HSPI)and modify its functional properties.Hemp seeds that were germinated for 0,1,3,and 5 days underwent alkaline extraction and protein isolation by isoelectric precipitation(IP)or ultrafiltration(UF).UF processing with a 100 nm membrane resulted in the loss of off-color pigments as well as vicilin proteins and small peptides~9 kDa,which changed the physicochemical properties and functionality of HSPI.We found that HSPIs from UF were lighter in color and higher in protein purity than isolates from IP,but lower in solubility.Germination paired with UF increased the water holding capacity by 2.3 times,from 1.06 to 2.46 g water/g isolate,while oil holding capacity was unaffected by germination and UF.UF resulted in protein isolates with decreased foaming capacity and increased gelation concentration compared to IP,but 5-day germinated HSPIs had statistically unchanged emulsifying activity indexes between the two processing methods.Germination and UF are thus presented as clean-label processing techniques to modify the composition and functionality of HSPIs.
