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
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.
