Computational tool-assisted primer design for real-time reverse transcription(RT)PCR(qPCR)analysis largely ignores the sequence similarities between sequences of homologous genes in a plant genome.It can lead to false...Computational tool-assisted primer design for real-time reverse transcription(RT)PCR(qPCR)analysis largely ignores the sequence similarities between sequences of homologous genes in a plant genome.It can lead to false confidence in the quality of the designed primers,which sometimes results in skipping the optimization steps for qPCR.However,the optimization of qPCR parameters plays an essential role in the efficiency,specificity,and sensitivity of each gene’s primers.Here,we proposed an optimized approach to sequentially optimizing primer sequences,annealing temperatures,primer concentrations,and cDNA concentration range for each reference(and target)gene.Our approach started with a sequence-specific primer design that should be based on the single-nucleotide polymorphisms(SNPs)present in all the homologous sequences for each of the reference(and target)genes under study.By combining the efficiency calibrated and standard curve methods with the 2−ΔΔCt method,the standard cDNA concentration curve with a logarithmic scale was obtained for each primer pair for each gene.As a result,an R 2≥0.9999 and the efficiency(E)=100±5% should be achieved for the best primer pair of each gene,which serve as the prerequisite for using the 2^(−ΔΔCt) method for data analysis.We applied our newly developed approach to identify the best reference genes in different tissues and at various inflorescence developmental stages of Tripidium ravennae,an ornamental and biomass grass,and validated their utility under varying abiotic stress conditions.We also applied this approach to test the expression stability of six reference genes in soybean under biotic stress treatment with Xanthomonas axonopodis pv.glycines(Xag).Thus,these case studies demonstrated the effectiveness of our optimized protocol for qPCR analysis.展开更多
The aim of this study was to produce bulk nanocrystalline Al/Al12（Fe,V）3Si alloys by mechanical alloying （MA） and subsequent hot pressing （HP） of elemental powders. A nanostructured Al-based solid solution was f...The aim of this study was to produce bulk nanocrystalline Al/Al12（Fe,V）3Si alloys by mechanical alloying （MA） and subsequent hot pressing （HP） of elemental powders. A nanostructured Al-based solid solution was formed by MA of elemental powders for 60 h. After HP of the as-milled powders at 550℃ for 20 min, the Al12（Fe,V）3Si phase was precipitated in a nanocrystalline Al matrix. Scanning electron microscopy （SEM） images of the bulk samples represented a homogeneous and uniform microstructure that was superior to those previously obtained by rapid solidification-powder metallurgy （RS-PM）. Nanostructured Al-8.5Fe-1.3V-1.7Si and Al-11.6Fe-1.3V-2.3Si alloys ex-hibited high HV hardness values of～205 and～254, respectively, which are significantly higher than those reported for the RS-PM counter-parts.展开更多
Fruit quality traits play a significant role in consumer preferences and consumption in blueberry(Vaccinium corymbosum L).The objectives of this study were to construct a high-density linkage map and to identify the u...Fruit quality traits play a significant role in consumer preferences and consumption in blueberry(Vaccinium corymbosum L).The objectives of this study were to construct a high-density linkage map and to identify the underlying genetic basis of fruit quality traits in blueberry.A total of 287 F_(1) individuals derived from a cross between two southern highbush blueberry cultivars,‘Reveille’and‘Arlen’,were phenotyped over three years(2016–2018)for fruit quality-related traits,including titratable acidity,pH,total soluble solids,and fruit weight.A high-density linkage map was constructed using 17k single nucleotide polymorphisms markers.The linkage map spanned a total of 1397 cM with an average inter-loci distance of 0.08 cM.The quantitative trait loci interval mapping based on the hidden Markov model identified 18 loci for fruit quality traits,including seven loci for fruit weight,three loci for titratable acidity,five loci for pH,and three loci for total soluble solids.Ten of these loci were detected in more than one year.These loci explained phenotypic variance ranging from 7 to 28% for titratable acidity and total soluble solid,and 8-13% for pH.However,the loci identified for fruit weight did not explain more than 10%of the phenotypic variance.We also reported the association between fruit quality traits and metabolites detected by Proton nuclear magnetic resonance analysis directly responsible for these fruit quality traits.Organic acids,citric acid,and quinic acid were significantly(P<0.05)and positively correlated with titratable acidity.Sugar molecules showed a strong and positive correlation with total soluble solids.Overall,the study dissected the genetic basis of fruit quality traits and established an association between these fruit quality traits and metabolites.展开更多
Size and shape are important properties of shrub crops such as blueberries,and they can be particularly useful for evaluating bush architecture suited to mechanical harvesting.The overall goal of this study was to dev...Size and shape are important properties of shrub crops such as blueberries,and they can be particularly useful for evaluating bush architecture suited to mechanical harvesting.The overall goal of this study was to develop a 3D imaging approach to measure size-related traits and bush shape that are relevant to mechanical harvesting.3D point clouds were acquired for 367 bushes from five genotype groups.Point cloud data were preprocessed to obtain clean bush points for characterizing bush architecture,including bush morphology(height,width,and volume),crown size,and shape descriptors(path curveλand five shape indices).One-dimensional traits(height,width,and crown size)had high correlations(R^(2)=0.88–0.95)between proposed method and manual measurements,whereas bush volume showed relatively lower correlations(R^(2)=0.78–0.85).These correlations suggested that the present approach was accurate in measuring one-dimensional size traits and acceptable in estimating three-dimensional bush volume.Statistical results demonstrated that the five genotype groups were statistically different in crown size and bush shape.The differences matched with human evaluation regarding optimal bush architecture for mechanical harvesting.In particular,a visualization tool could be generated using crown size and path curveλ,which showed great potential of determining bush architecture suitable for mechanical harvesting quickly.Therefore,the processing pipeline of 3D point cloud data presented in this study is an effective tool for blueberry breeding programs(in particular for mechanical harvesting)and farm management.展开更多
The Capsicum genus(Pepper)is a part of the Solanacae family.It has been important in many cultures worldwide for its key nutritional components and uses as spices,medicines,ornamentals and vegetables.Worldwide populat...The Capsicum genus(Pepper)is a part of the Solanacae family.It has been important in many cultures worldwide for its key nutritional components and uses as spices,medicines,ornamentals and vegetables.Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land.These conditions require increased efficiency in pepper breeding to deal with these imminent challenges.Through resequencing of inbred lines we have completed a valuable haplotype map(HapMap)for the pepper genome based on single-nucleotide polymorphisms(SNP).The identified SNPs were annotated and classified based on their gene annotation in the pepper draft genome sequence and phenotype of the sequenced inbred lines.A selection of one marker per gene model was utilized to create the PepperSNP16K array,which simultaneously genotyped 16405 SNPs,of which 90.7%were found to be informative.A set of 84 inbred and hybrid lines and a mapping population of 90 interspecific F2 individuals were utilized to validate the array.Diversity analysis of the inbred lines shows a distinct separation of bell versus chile/hot pepper types and separates them into five distinct germplasm groups.The interspecific population created between Tabasco(C.frutescens chile type)and P4(C.annuum blocky type)produced a linkage map with 5546 markers separated into 1361 bins on twelve 12 linkage groups representing 1392.3 cM.This publically available genotyping platform can be used to rapidly assess a large number of markers in a reproducible high-throughput manner for pepper.As a standardized tool for genetic analyses,the PepperSNP16K can be used worldwide to share findings and analyze QTLs for important traits leading to continued improvement of pepper for consumers.Data and information on the array are available through the Solanaceae Genomics Network.展开更多
The void formation and plastic deformation micromechanisms of a cold-rolled DP600 steel during tensile loading were studied by scanning electron microscopy(SEM) and electron backscatter diffraction(EBSD).The SEM obser...The void formation and plastic deformation micromechanisms of a cold-rolled DP600 steel during tensile loading were studied by scanning electron microscopy(SEM) and electron backscatter diffraction(EBSD).The SEM observations revealed that the main void nucleation mechanism in the DP600 steel is decohesion at the ferrite-martensite interfaces.The voids were mostly observed between the closely spaced martensite islands situated at the boundaries of relatively finer ferrite grains.The EBSD results indicated a strain gradient developed from the ferrite-martensite and ferrite-ferrite interfaces into the interior of ferrite grains during the tensile deformation,which led to a stress concentration at these interfaces.Moreover,it was demonstrated that local misorientation inside the finer ferrite grains surrounded by martensite islands was higher than that for the coarser ferrite grains,which made the former more prone to void initiation.展开更多
Tribological behavior of nanostructured pure Al and Al–Al12（Fe,V）3Si alloys containing 27（FVS0812） and 37（FVS1212） vol% of Al12（Fe,V）3Si precipitates was investigated. All samples were prepared using mechanic...Tribological behavior of nanostructured pure Al and Al–Al12（Fe,V）3Si alloys containing 27（FVS0812） and 37（FVS1212） vol% of Al12（Fe,V）3Si precipitates was investigated. All samples were prepared using mechanical alloying followed by hot pressing. Wear tests were performed at room temperature using a pin-on-disk machine. Results showed that the presence of Al12（Fe,V）3Si precipitates increases the wear resistance of nanostructured Al, and the wear resistance increases with increasing the Al12（Fe,V）3Si content. Scanning electron microscopy images of worn surfaces and wear debris demonstrated that abrasion and adhesion are the governing wear mechanisms for the nanostructured FVS0812 alloy at 2 and 5 N normal loads, whereas for the nanostructured FVS1212 alloy, the dominant wear mechanism is abrasion at these loads. A mechanically mixed layer（MML） containing Fe and O was formed on the worn surfaces of FVS0812 and FVS1212 samples at 10 N normal load. Formation and delamination of MML controls the wear behavior of these samples at the normal load of 10 N. It is also found that the presence of Al12（Fe,V）3Si precipitates decreases the friction coefficient of nanostructured Al.展开更多
基金The authors thank the USDA National Institute of Food and Agriculture Hatch project 02685 and North Carolina State University for the startup funds to the Liu laboratorythe NSFC fund 31871646 to the Zhao laboratory。
文摘Computational tool-assisted primer design for real-time reverse transcription(RT)PCR(qPCR)analysis largely ignores the sequence similarities between sequences of homologous genes in a plant genome.It can lead to false confidence in the quality of the designed primers,which sometimes results in skipping the optimization steps for qPCR.However,the optimization of qPCR parameters plays an essential role in the efficiency,specificity,and sensitivity of each gene’s primers.Here,we proposed an optimized approach to sequentially optimizing primer sequences,annealing temperatures,primer concentrations,and cDNA concentration range for each reference(and target)gene.Our approach started with a sequence-specific primer design that should be based on the single-nucleotide polymorphisms(SNPs)present in all the homologous sequences for each of the reference(and target)genes under study.By combining the efficiency calibrated and standard curve methods with the 2−ΔΔCt method,the standard cDNA concentration curve with a logarithmic scale was obtained for each primer pair for each gene.As a result,an R 2≥0.9999 and the efficiency(E)=100±5% should be achieved for the best primer pair of each gene,which serve as the prerequisite for using the 2^(−ΔΔCt) method for data analysis.We applied our newly developed approach to identify the best reference genes in different tissues and at various inflorescence developmental stages of Tripidium ravennae,an ornamental and biomass grass,and validated their utility under varying abiotic stress conditions.We also applied this approach to test the expression stability of six reference genes in soybean under biotic stress treatment with Xanthomonas axonopodis pv.glycines(Xag).Thus,these case studies demonstrated the effectiveness of our optimized protocol for qPCR analysis.
文摘The aim of this study was to produce bulk nanocrystalline Al/Al12（Fe,V）3Si alloys by mechanical alloying （MA） and subsequent hot pressing （HP） of elemental powders. A nanostructured Al-based solid solution was formed by MA of elemental powders for 60 h. After HP of the as-milled powders at 550℃ for 20 min, the Al12（Fe,V）3Si phase was precipitated in a nanocrystalline Al matrix. Scanning electron microscopy （SEM） images of the bulk samples represented a homogeneous and uniform microstructure that was superior to those previously obtained by rapid solidification-powder metallurgy （RS-PM）. Nanostructured Al-8.5Fe-1.3V-1.7Si and Al-11.6Fe-1.3V-2.3Si alloys ex-hibited high HV hardness values of～205 and～254, respectively, which are significantly higher than those reported for the RS-PM counter-parts.
基金This research was supported by the Foundation for Food and Agriculture Research(FFAR)under award number 534667.MI and MAL were also supported by the United States Department of Agriculture National Institute of Food and Agriculture,Hatch project 1008691the National Institute of Food and Agriculture,United States Department of Agriculture,under award number 2019-51181-30015,project“VacciniumCAP:Leveraging genetic and genomic resources to enable development of blueberry and cranberry cultivars with improved fruit quality attributes”.
文摘Fruit quality traits play a significant role in consumer preferences and consumption in blueberry(Vaccinium corymbosum L).The objectives of this study were to construct a high-density linkage map and to identify the underlying genetic basis of fruit quality traits in blueberry.A total of 287 F_(1) individuals derived from a cross between two southern highbush blueberry cultivars,‘Reveille’and‘Arlen’,were phenotyped over three years(2016–2018)for fruit quality-related traits,including titratable acidity,pH,total soluble solids,and fruit weight.A high-density linkage map was constructed using 17k single nucleotide polymorphisms markers.The linkage map spanned a total of 1397 cM with an average inter-loci distance of 0.08 cM.The quantitative trait loci interval mapping based on the hidden Markov model identified 18 loci for fruit quality traits,including seven loci for fruit weight,three loci for titratable acidity,five loci for pH,and three loci for total soluble solids.Ten of these loci were detected in more than one year.These loci explained phenotypic variance ranging from 7 to 28% for titratable acidity and total soluble solid,and 8-13% for pH.However,the loci identified for fruit weight did not explain more than 10%of the phenotypic variance.We also reported the association between fruit quality traits and metabolites detected by Proton nuclear magnetic resonance analysis directly responsible for these fruit quality traits.Organic acids,citric acid,and quinic acid were significantly(P<0.05)and positively correlated with titratable acidity.Sugar molecules showed a strong and positive correlation with total soluble solids.Overall,the study dissected the genetic basis of fruit quality traits and established an association between these fruit quality traits and metabolites.
基金supported by the USDA National Institute of Food and Agriculture Specialty Crop Research Initiative(Award No:2014-51181-22383).
文摘Size and shape are important properties of shrub crops such as blueberries,and they can be particularly useful for evaluating bush architecture suited to mechanical harvesting.The overall goal of this study was to develop a 3D imaging approach to measure size-related traits and bush shape that are relevant to mechanical harvesting.3D point clouds were acquired for 367 bushes from five genotype groups.Point cloud data were preprocessed to obtain clean bush points for characterizing bush architecture,including bush morphology(height,width,and volume),crown size,and shape descriptors(path curveλand five shape indices).One-dimensional traits(height,width,and crown size)had high correlations(R^(2)=0.88–0.95)between proposed method and manual measurements,whereas bush volume showed relatively lower correlations(R^(2)=0.78–0.85).These correlations suggested that the present approach was accurate in measuring one-dimensional size traits and acceptable in estimating three-dimensional bush volume.Statistical results demonstrated that the five genotype groups were statistically different in crown size and bush shape.The differences matched with human evaluation regarding optimal bush architecture for mechanical harvesting.In particular,a visualization tool could be generated using crown size and path curveλ,which showed great potential of determining bush architecture suitable for mechanical harvesting quickly.Therefore,the processing pipeline of 3D point cloud data presented in this study is an effective tool for blueberry breeding programs(in particular for mechanical harvesting)and farm management.
文摘The Capsicum genus(Pepper)is a part of the Solanacae family.It has been important in many cultures worldwide for its key nutritional components and uses as spices,medicines,ornamentals and vegetables.Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land.These conditions require increased efficiency in pepper breeding to deal with these imminent challenges.Through resequencing of inbred lines we have completed a valuable haplotype map(HapMap)for the pepper genome based on single-nucleotide polymorphisms(SNP).The identified SNPs were annotated and classified based on their gene annotation in the pepper draft genome sequence and phenotype of the sequenced inbred lines.A selection of one marker per gene model was utilized to create the PepperSNP16K array,which simultaneously genotyped 16405 SNPs,of which 90.7%were found to be informative.A set of 84 inbred and hybrid lines and a mapping population of 90 interspecific F2 individuals were utilized to validate the array.Diversity analysis of the inbred lines shows a distinct separation of bell versus chile/hot pepper types and separates them into five distinct germplasm groups.The interspecific population created between Tabasco(C.frutescens chile type)and P4(C.annuum blocky type)produced a linkage map with 5546 markers separated into 1361 bins on twelve 12 linkage groups representing 1392.3 cM.This publically available genotyping platform can be used to rapidly assess a large number of markers in a reproducible high-throughput manner for pepper.As a standardized tool for genetic analyses,the PepperSNP16K can be used worldwide to share findings and analyze QTLs for important traits leading to continued improvement of pepper for consumers.Data and information on the array are available through the Solanaceae Genomics Network.
文摘The void formation and plastic deformation micromechanisms of a cold-rolled DP600 steel during tensile loading were studied by scanning electron microscopy(SEM) and electron backscatter diffraction(EBSD).The SEM observations revealed that the main void nucleation mechanism in the DP600 steel is decohesion at the ferrite-martensite interfaces.The voids were mostly observed between the closely spaced martensite islands situated at the boundaries of relatively finer ferrite grains.The EBSD results indicated a strain gradient developed from the ferrite-martensite and ferrite-ferrite interfaces into the interior of ferrite grains during the tensile deformation,which led to a stress concentration at these interfaces.Moreover,it was demonstrated that local misorientation inside the finer ferrite grains surrounded by martensite islands was higher than that for the coarser ferrite grains,which made the former more prone to void initiation.
文摘Tribological behavior of nanostructured pure Al and Al–Al12（Fe,V）3Si alloys containing 27（FVS0812） and 37（FVS1212） vol% of Al12（Fe,V）3Si precipitates was investigated. All samples were prepared using mechanical alloying followed by hot pressing. Wear tests were performed at room temperature using a pin-on-disk machine. Results showed that the presence of Al12（Fe,V）3Si precipitates increases the wear resistance of nanostructured Al, and the wear resistance increases with increasing the Al12（Fe,V）3Si content. Scanning electron microscopy images of worn surfaces and wear debris demonstrated that abrasion and adhesion are the governing wear mechanisms for the nanostructured FVS0812 alloy at 2 and 5 N normal loads, whereas for the nanostructured FVS1212 alloy, the dominant wear mechanism is abrasion at these loads. A mechanically mixed layer（MML） containing Fe and O was formed on the worn surfaces of FVS0812 and FVS1212 samples at 10 N normal load. Formation and delamination of MML controls the wear behavior of these samples at the normal load of 10 N. It is also found that the presence of Al12（Fe,V）3Si precipitates decreases the friction coefficient of nanostructured Al.
