Most important agricultural traits of crops are controlled by many genes. These traits have complicated genetic basis and are difficult for genetic analysis. Due to application of molecular marker techniques in the la...Most important agricultural traits of crops are controlled by many genes. These traits have complicated genetic basis and are difficult for genetic analysis. Due to application of molecular marker techniques in the last two decades, genetic and molecular dissection of quantitative traits has become possible. In this paper, recent progress on mapping of quantitative trait loci in crops was reviewed.展开更多
When alien DNA inserts into cotton genome in multi-copy manner,several QTL in cotton genome are disrupted,which are called dQTL in this study.Transgenic mutant line is near-isogenic to its recipient which is divergent...When alien DNA inserts into cotton genome in multi-copy manner,several QTL in cotton genome are disrupted,which are called dQTL in this study.Transgenic mutant line is near-isogenic to its recipient which is divergent for the dQTL from remaining QTL.So,a set of data from a展开更多
Cotton(Gossypium spp.) is the leading fiber crop,and an important source of the important edible oil and protein meals in the world.Complex genetics and strong environmental effects hinder
Creutzfeldt-Jakob disease(CJD)is a rare neurodegenerative disorder characterized by abnormalities in the prion protein(PrP),the most common form of human prion disease.Although Genome-Wide Association Studies(GWAS)hav...Creutzfeldt-Jakob disease(CJD)is a rare neurodegenerative disorder characterized by abnormalities in the prion protein(PrP),the most common form of human prion disease.Although Genome-Wide Association Studies(GWAS)have identified numerous risk genes for CJD,the mechanisms underlying these risk loci remain poorly understood.This study aims to elucidate novel genetically prioritized candidate proteins associated with CJD in the human brain through an integrative analytical pipeline.Utilizing datasets from Protein Quantitative Trait Loci(pQTL)(NpQTL1=152,NpQTL2=376),expression QTL(eQTL)(N=452),and the CJD GWAS(NCJD=4110,NControls=13569),we implemented a systematic analytical pipeline.This pipeline included Proteome-Wide Association Study(PWAS),Mendelian randomization(MR),Bayesian colocalization,and Transcriptome-Wide Association Study(TWAS)to identify novel genetically prioritized candidate proteins implicated in CJD pathogenesis within the brain.Through PWAS,we identified that the altered abundance of six brain proteins was significantly associated with CJD.Two genes,STX6 and PDIA4,were established as lead causal genes for CJD,supported by robust evidence(False Discovery Rate<0.05 in MR analysis;PP4/(PP3+PP4)≥0.75 in Bayesian colocalization).Specifically,elevated levels of STX6 and PDIA4 were associated with an increased risk of CJD.Additionally,TWAS demonstrated that STX6 and PDIA4 were associated with CJD at the transcriptional level.展开更多
Background Cotton is an important cash crop in China and a key component of the global textile market.Verticil-lium wilt is a major factor affecting cotton yield.Single nucleotide polymorphism(SNP)markers and phenotyp...Background Cotton is an important cash crop in China and a key component of the global textile market.Verticil-lium wilt is a major factor affecting cotton yield.Single nucleotide polymorphism(SNP)markers and phenotypic data can be used to identify genetic markers and loci associated with cotton resistance to Verticillium wilt.We used eight upland cotton parent materials in this study to construct a multiparent advanced generation inter-cross(MAGIC)population comprising 320 lines.The Verticillium wilt resistance of the MAGIC population was identified in the green-house in 2019,and the average relative disease index(ARDI)was calculated.A genome-wide association study(GWAS)was performed to discover SNP markers/genes associated with Verticillium wilt resistance.Results ARDI of the MAGIC population showed wide variation,ranging from 16.7 to 79.4 across three replicates.This variation reflected a diverse range of resistance to Verticillium wilt within the population.Analysis of distribution pat-terns across the environments revealed consistent trends,with coefficients of variation between 12.25%and 21.96%.Families with higher ARDI values,indicating stronger resistance,were more common,likely due to genetic diver-sity and environmental factors.Population structure analysis divided the MAGIC population into three subgroups,with Group I showing higher genetic variation and Groups II and III displaying more uniform resistance performance.Principal component analysis(PCA)confirmed these divisions,highlighting the genetic diversity underlying Verticil-lium wilt resistance.Through GWAS,we identified 19 SNPs significantly associated with Verticillium wilt resistance,distributed across three chromosomes.The screening of candidate genes was performed on the transcriptome derived from resistant and susceptible cultivars,combined with gene annotation and tissue expression patterns,and two key candidate genes,Ghir_A01G006660 and Ghir_A02G008980,were found to be potentially associated with Verticillium wilt resistance.This suggests that these two candidate genes may play an important role in responding to Verticillium wilt.Conclusion This study aims to dissect the genetic basis of Verticillium wilt resistance in cotton by using a MAGIC population and GWAS.The study seeks to provide valuable genetic resources for marker-assisted breeding and enhance the understanding of resistance mechanisms to improve cotton resilience against Verticillium wilt.展开更多
Plant height in cucumber is not only an important trait for breeding,but also one of the model traits suitable for the study of developmental biology.Amplified fragment length polymorphism(AFLP)and simple sequence rep...Plant height in cucumber is not only an important trait for breeding,but also one of the model traits suitable for the study of developmental biology.Amplified fragment length polymorphism(AFLP)and simple sequence repeat(SSR)markers techniques were applied for the construction of genetic linkage maps in cucumber.To understand the dwarf trait genetic basis in cucumber,the quantitative trait loci(QTL)were identified using F_6 recombinant inbred line populations(RILs)comprising 336 lines from the cross between the two cultivars D0462(the dwarf)and DN129(the vine).In total,six SSR markers and 15 AFLP markers were detected on the five linkage groups covering 152.8 cM with a mean marker interval of 7.28 cM.Only one QTL was found to be linked with plant height and the dwarf trait locus remained in the fourth linkage group.The contributory percentage of the single QTL to plant height was 11.39%.展开更多
Cotton,an important industrial crop cultivated in more than 70 countries,plays a major role in the livelihood of millions of farmers and industrialists.Cotton is mainly grown for its fiber,an economic component that c...Cotton,an important industrial crop cultivated in more than 70 countries,plays a major role in the livelihood of millions of farmers and industrialists.Cotton is mainly grown for its fiber,an economic component that can be differentiated from its epidermal cells in the outer integument of a developing seed.Fiber length,fiber strength,and fiber fineness are three main attributes that contribute to the quality of cotton fibers.Recent advancements in genomics have identified key genes,which are the most important factors that govern these three traits,can be introduced into cultivars of interest via gene editing,marker-assisted selection,and transgenics,thus the narrow genetic background of cotton can be addressed and its fiber quality traits can be enhanced.Over the past two decades,quantitative trait loci(QTLs)have been mapped for different fiber traits,approximately 1850 QTLs have been mapped for fiber length,fiber strength,and fineness among which a few genes have been edited for quality improvement in cotton.In this background,the current review covers the development and the factors that influence these traits,along with the reported genes,QTLs,and the edited genomes for trait improvement.展开更多
Field trials with a set of 108 doubled haploid lines(DHs) derived from a cross between the Chinese winter wheat cvs.CA9613 and H1488 were run at Beijing(China).Phenotypic data were recorded for major agronomic yield t...Field trials with a set of 108 doubled haploid lines(DHs) derived from a cross between the Chinese winter wheat cvs.CA9613 and H1488 were run at Beijing(China).Phenotypic data were recorded for major agronomic yield traits,i.e.grain weight per ear,grain number per ear and thousand grain weight(Tgw) in two field trials at Beijing.Based on the phenotypic data and a genetic map comprising 168 SSR markers,an analysis of quantitative trait loci(QTL) was carried out for yield and yield parameters using the composite interval mapping(CIM) approach.A total of 14 QTL were detected for these traits across two environments.Four of these QTL located on chromosomes 1A and 2B,respectively,exhibited pleiotropic effects.Loci showing pleiotropic effects will be very useful for understanding the homeologous relationships of QTL and designing an appropriate marker-assisted selection programme by multi-trait selection in order to accumulate("pyramide") favorable alleles at different loci.展开更多
Hefeng 25 variety with low vitamin E content in Heilongjiang Province and Bayfield variety with high vitamin E content in Canada were crossed.A total of 144 F_(2:7) recombinant inbred lines(RILs)were used as materials...Hefeng 25 variety with low vitamin E content in Heilongjiang Province and Bayfield variety with high vitamin E content in Canada were crossed.A total of 144 F_(2:7) recombinant inbred lines(RILs)were used as materials.The genetic linkage mapping of soybean vitamin E was constructed.Soybean varieties were marker-assisted selected in the interval of refined quantitative trait locus(QTLs).QTLs were identified in α-,γ-,δ-and the total tocopherol contents of soybean seeds.Fine QTLs of soybean vitamin E content were identified in the interval between Sat_239 and Satt022 on N linkage group.It was valuable to narrow the interval by marker-assisted selection(MAS).There were seven major QTLs of vitamin E content in soybean.MAS related to vitamin E content in soybean was carried out in the intervals between Sat_239 and Satt022.Considering all the kinds of agronomic traits,six strains with high yield and good quality of vitamin E were chosen,numbered 4,54,104,114,122 and 135.展开更多
Soybean seed oil has always been the primary focus of researches on improving the quality of soybean.Triacylglycerol,which is composed of fatty acids and glycerol,serves as the main storage form of soybean seed oil.Th...Soybean seed oil has always been the primary focus of researches on improving the quality of soybean.Triacylglycerol,which is composed of fatty acids and glycerol,serves as the main storage form of soybean seed oil.Therefore,the biosynthesis of fatty acids and the assembly of triacylglycerol significantly affect the quality of soybean seed oil.The process of soybean seed oil synthesis was comprehensively analyzed by examining the synthesis and activation of acetyl-CoA,fatty acid biosynthesis and desaturation,triacylglycerol assembly,and other related processes,additionally,this analysis identified the key enzymes and transcription factors involved in each link of the oil synthesis process.It was found that the researches on the key enzymes of carbon source regulation,pyruvate dehydrogenase complex and acetyl-CoA carboxylase,in the genetic network of soybean seed oil synthesis,were somewhat limited.Analyzing their structures and functions would aid in further understanding the molecular mechanism of soybean fatty acid synthesis,which would be beneficial for enhancing soybean oil content and synthesis efficiency.Based on summarizing the results of genetic analysis of soybean oil and fatty acids,the prospects for mechanism analysis and advancements in biological breeding techniques for improving soybean oil quality at the molecular level were discussed.展开更多
文摘Most important agricultural traits of crops are controlled by many genes. These traits have complicated genetic basis and are difficult for genetic analysis. Due to application of molecular marker techniques in the last two decades, genetic and molecular dissection of quantitative traits has become possible. In this paper, recent progress on mapping of quantitative trait loci in crops was reviewed.
文摘When alien DNA inserts into cotton genome in multi-copy manner,several QTL in cotton genome are disrupted,which are called dQTL in this study.Transgenic mutant line is near-isogenic to its recipient which is divergent for the dQTL from remaining QTL.So,a set of data from a
文摘Cotton(Gossypium spp.) is the leading fiber crop,and an important source of the important edible oil and protein meals in the world.Complex genetics and strong environmental effects hinder
文摘Creutzfeldt-Jakob disease(CJD)is a rare neurodegenerative disorder characterized by abnormalities in the prion protein(PrP),the most common form of human prion disease.Although Genome-Wide Association Studies(GWAS)have identified numerous risk genes for CJD,the mechanisms underlying these risk loci remain poorly understood.This study aims to elucidate novel genetically prioritized candidate proteins associated with CJD in the human brain through an integrative analytical pipeline.Utilizing datasets from Protein Quantitative Trait Loci(pQTL)(NpQTL1=152,NpQTL2=376),expression QTL(eQTL)(N=452),and the CJD GWAS(NCJD=4110,NControls=13569),we implemented a systematic analytical pipeline.This pipeline included Proteome-Wide Association Study(PWAS),Mendelian randomization(MR),Bayesian colocalization,and Transcriptome-Wide Association Study(TWAS)to identify novel genetically prioritized candidate proteins implicated in CJD pathogenesis within the brain.Through PWAS,we identified that the altered abundance of six brain proteins was significantly associated with CJD.Two genes,STX6 and PDIA4,were established as lead causal genes for CJD,supported by robust evidence(False Discovery Rate<0.05 in MR analysis;PP4/(PP3+PP4)≥0.75 in Bayesian colocalization).Specifically,elevated levels of STX6 and PDIA4 were associated with an increased risk of CJD.Additionally,TWAS demonstrated that STX6 and PDIA4 were associated with CJD at the transcriptional level.
基金supported by funding from the fund for National Key Research and Development Program of China(2023YFD2301203-05)National Natural Science Foundation of China(32260510)+3 种基金Special Financial Project for Seed Industry Development in the Autonomous Region(BNZJ2024-10,BNZJ2024-30)Key Project for Science and Technology Development of Shihezi city,Xinjiang Production and Construction Crops(2022NY01)Shihezi University high-level talent research project(RCZK202337)Science and Technol-ogy Planning of Shuanghe city,Xinjiang Production and Construction Crops(2021NY02).
文摘Background Cotton is an important cash crop in China and a key component of the global textile market.Verticil-lium wilt is a major factor affecting cotton yield.Single nucleotide polymorphism(SNP)markers and phenotypic data can be used to identify genetic markers and loci associated with cotton resistance to Verticillium wilt.We used eight upland cotton parent materials in this study to construct a multiparent advanced generation inter-cross(MAGIC)population comprising 320 lines.The Verticillium wilt resistance of the MAGIC population was identified in the green-house in 2019,and the average relative disease index(ARDI)was calculated.A genome-wide association study(GWAS)was performed to discover SNP markers/genes associated with Verticillium wilt resistance.Results ARDI of the MAGIC population showed wide variation,ranging from 16.7 to 79.4 across three replicates.This variation reflected a diverse range of resistance to Verticillium wilt within the population.Analysis of distribution pat-terns across the environments revealed consistent trends,with coefficients of variation between 12.25%and 21.96%.Families with higher ARDI values,indicating stronger resistance,were more common,likely due to genetic diver-sity and environmental factors.Population structure analysis divided the MAGIC population into three subgroups,with Group I showing higher genetic variation and Groups II and III displaying more uniform resistance performance.Principal component analysis(PCA)confirmed these divisions,highlighting the genetic diversity underlying Verticil-lium wilt resistance.Through GWAS,we identified 19 SNPs significantly associated with Verticillium wilt resistance,distributed across three chromosomes.The screening of candidate genes was performed on the transcriptome derived from resistant and susceptible cultivars,combined with gene annotation and tissue expression patterns,and two key candidate genes,Ghir_A01G006660 and Ghir_A02G008980,were found to be potentially associated with Verticillium wilt resistance.This suggests that these two candidate genes may play an important role in responding to Verticillium wilt.Conclusion This study aims to dissect the genetic basis of Verticillium wilt resistance in cotton by using a MAGIC population and GWAS.The study seeks to provide valuable genetic resources for marker-assisted breeding and enhance the understanding of resistance mechanisms to improve cotton resilience against Verticillium wilt.
基金Supported by the"Academic Backbone"Project of Northeast Agricultural University(18XG06)Supporting Certificate of Heilongjiang Postdoctoral Scientific Research Developmental Fund(LBH-Q16021)the Natural Science Foundation of Heilongjiang Province,China(LH2019C033)。
文摘Plant height in cucumber is not only an important trait for breeding,but also one of the model traits suitable for the study of developmental biology.Amplified fragment length polymorphism(AFLP)and simple sequence repeat(SSR)markers techniques were applied for the construction of genetic linkage maps in cucumber.To understand the dwarf trait genetic basis in cucumber,the quantitative trait loci(QTL)were identified using F_6 recombinant inbred line populations(RILs)comprising 336 lines from the cross between the two cultivars D0462(the dwarf)and DN129(the vine).In total,six SSR markers and 15 AFLP markers were detected on the five linkage groups covering 152.8 cM with a mean marker interval of 7.28 cM.Only one QTL was found to be linked with plant height and the dwarf trait locus remained in the fourth linkage group.The contributory percentage of the single QTL to plant height was 11.39%.
文摘Cotton,an important industrial crop cultivated in more than 70 countries,plays a major role in the livelihood of millions of farmers and industrialists.Cotton is mainly grown for its fiber,an economic component that can be differentiated from its epidermal cells in the outer integument of a developing seed.Fiber length,fiber strength,and fiber fineness are three main attributes that contribute to the quality of cotton fibers.Recent advancements in genomics have identified key genes,which are the most important factors that govern these three traits,can be introduced into cultivars of interest via gene editing,marker-assisted selection,and transgenics,thus the narrow genetic background of cotton can be addressed and its fiber quality traits can be enhanced.Over the past two decades,quantitative trait loci(QTLs)have been mapped for different fiber traits,approximately 1850 QTLs have been mapped for fiber length,fiber strength,and fineness among which a few genes have been edited for quality improvement in cotton.In this background,the current review covers the development and the factors that influence these traits,along with the reported genes,QTLs,and the edited genomes for trait improvement.
文摘Field trials with a set of 108 doubled haploid lines(DHs) derived from a cross between the Chinese winter wheat cvs.CA9613 and H1488 were run at Beijing(China).Phenotypic data were recorded for major agronomic yield traits,i.e.grain weight per ear,grain number per ear and thousand grain weight(Tgw) in two field trials at Beijing.Based on the phenotypic data and a genetic map comprising 168 SSR markers,an analysis of quantitative trait loci(QTL) was carried out for yield and yield parameters using the composite interval mapping(CIM) approach.A total of 14 QTL were detected for these traits across two environments.Four of these QTL located on chromosomes 1A and 2B,respectively,exhibited pleiotropic effects.Loci showing pleiotropic effects will be very useful for understanding the homeologous relationships of QTL and designing an appropriate marker-assisted selection programme by multi-trait selection in order to accumulate("pyramide") favorable alleles at different loci.
基金Supported by Chinese National Natural Science Foundation(31701446)。
文摘Hefeng 25 variety with low vitamin E content in Heilongjiang Province and Bayfield variety with high vitamin E content in Canada were crossed.A total of 144 F_(2:7) recombinant inbred lines(RILs)were used as materials.The genetic linkage mapping of soybean vitamin E was constructed.Soybean varieties were marker-assisted selected in the interval of refined quantitative trait locus(QTLs).QTLs were identified in α-,γ-,δ-and the total tocopherol contents of soybean seeds.Fine QTLs of soybean vitamin E content were identified in the interval between Sat_239 and Satt022 on N linkage group.It was valuable to narrow the interval by marker-assisted selection(MAS).There were seven major QTLs of vitamin E content in soybean.MAS related to vitamin E content in soybean was carried out in the intervals between Sat_239 and Satt022.Considering all the kinds of agronomic traits,six strains with high yield and good quality of vitamin E were chosen,numbered 4,54,104,114,122 and 135.
基金Supported by the Heilongjiang Natural Science Foundation Joint Guidance Project(LH2021C028)。
文摘Soybean seed oil has always been the primary focus of researches on improving the quality of soybean.Triacylglycerol,which is composed of fatty acids and glycerol,serves as the main storage form of soybean seed oil.Therefore,the biosynthesis of fatty acids and the assembly of triacylglycerol significantly affect the quality of soybean seed oil.The process of soybean seed oil synthesis was comprehensively analyzed by examining the synthesis and activation of acetyl-CoA,fatty acid biosynthesis and desaturation,triacylglycerol assembly,and other related processes,additionally,this analysis identified the key enzymes and transcription factors involved in each link of the oil synthesis process.It was found that the researches on the key enzymes of carbon source regulation,pyruvate dehydrogenase complex and acetyl-CoA carboxylase,in the genetic network of soybean seed oil synthesis,were somewhat limited.Analyzing their structures and functions would aid in further understanding the molecular mechanism of soybean fatty acid synthesis,which would be beneficial for enhancing soybean oil content and synthesis efficiency.Based on summarizing the results of genetic analysis of soybean oil and fatty acids,the prospects for mechanism analysis and advancements in biological breeding techniques for improving soybean oil quality at the molecular level were discussed.
