The main active components of ginseng are ginsenosides,which play significant roles in treating cardiovascular diseases,cancer,and providing antioxidant effects.Ginsenosides are primarily synthesized through the mevalo...The main active components of ginseng are ginsenosides,which play significant roles in treating cardiovascular diseases,cancer,and providing antioxidant effects.Ginsenosides are primarily synthesized through the mevalo-nate pathway and the methylerythritol phosphate pathway.Many key enzyme genes involved in this biosynthetic process have been cloned and validated,yet the regulatory functions of transcription factors remain unclear.The C_(2)H_(2)-type zincfinger protein family,one of the largest families of transcription factors,is crucial in plant growth and development,response to biotic and abiotic stresses,and regulation of secondary metabolism.This study,based on the ginseng transcriptome database from Jilin,conducted a correlation analysis between the expression levels of PgZFPs genes in the Jilin ginseng C_(2)H_(2)-type zincfinger protein family and ginsenoside content,a gen-ome-wide association study of PgZFPs,and co-expression analysis of PgZFPs with validated key enzyme genes.Ultimately,five candidate genes involved in ginsenoside biosynthesis were identified.The involvement of PgZFP27 and PgZFP-59-02 genes from the PgZFPs family in the biosynthesis of ginsenosides was validated through in vitro methyl jasmonate(MeJA)induction experiments.This result provides new genetic resources for the biosynthesis of ginsenosides.展开更多
Family-based tests of association between a genetic marker and a disease constitute a common design to dissect the genetic architecture of complex traits. The FBAT software is one of the most popular tools to perform ...Family-based tests of association between a genetic marker and a disease constitute a common design to dissect the genetic architecture of complex traits. The FBAT software is one of the most popular tools to perform such studies. However, researchers are also often interested in the genetic contribution to a more specific manifestation of the phenotype (e.g. severe vs. non-severe form) known as a secondary outcome. Here, what we demonstrate is the limited power of the classical formulation of the FBAT statistic to detect the effect of genetic variants that influence a secondary outcome, in particular when these variants also impact on the onset of the disease, the primary outcome. We prove that this loss of power is driven by an implicit hypothesis, and we propose a derivation of the original FBAT statistic, free from this implicit hypothesis. Finally, we demonstrate analytically that our new statistic is robust and more powerful than FBAT for the detection of association between a genetic variant and a secondary outcome.展开更多
Background:Cotton is the source of natural fibers globally,fulfilling 90%of the textile industry’s requirements.However,fiber development is a complex biological process comprising four stages.Fiber develops from a s...Background:Cotton is the source of natural fibers globally,fulfilling 90%of the textile industry’s requirements.However,fiber development is a complex biological process comprising four stages.Fiber develops from a single cell,and cell elongation is a vital process in fiber development.Therefore,it is pertinent to understand and exploit mechanisms underlying cell elongation during fiber development.A previous report about cell division control protein 42(CDC-42)with its key role in cell elongation in eukaryotes inspired us to explore its homologs Rho GTPases for understanding of cell elongation during cotton fiber development.Result:We classified 2066 Rho proteins from 8 Gossypium species into 5 and 8 groups within A and D sub-genomes,respectively.Asymmetric evolution of Rho members was observed among five tetraploids.Population fixation statistics between two short and long fiber genotypes identified highly diverged regions encompassing 34 Rho genes in G.hirustum,and 31 of them were retained through further validation by genome wide association analysis(GWAS).Moreover,a weighted gene co-expression network characterized genome-wide expression patteren of Rho genes based on previously published transcriptome data.Twenty Rho genes from five modules were identified as hub genes which were potentially related to fiber development.Interaction networks of 5 Rho genes based on transcriptional abundance and gene ontology(GO)enrichment emphasized the involvement of Rho in cell wall biosynthesis,fatty acid elongation,and other biological processes.Conclusion:Our study characterized the Rho proteins in cotton,provided insights into the cell elongation of cotton fiber and potential application in cotton fiber improvement.展开更多
基金This work was supported by the Department of Science and Technology of Jilin Province(20240101227JC,20210402043GH,20200801063GH,20190201264JC,20190103104JH,20180414077GH,and 20180101027JC)the Development and Reform Commission of Jilin Province(2016C064 and 2018C047-3).
文摘The main active components of ginseng are ginsenosides,which play significant roles in treating cardiovascular diseases,cancer,and providing antioxidant effects.Ginsenosides are primarily synthesized through the mevalo-nate pathway and the methylerythritol phosphate pathway.Many key enzyme genes involved in this biosynthetic process have been cloned and validated,yet the regulatory functions of transcription factors remain unclear.The C_(2)H_(2)-type zincfinger protein family,one of the largest families of transcription factors,is crucial in plant growth and development,response to biotic and abiotic stresses,and regulation of secondary metabolism.This study,based on the ginseng transcriptome database from Jilin,conducted a correlation analysis between the expression levels of PgZFPs genes in the Jilin ginseng C_(2)H_(2)-type zincfinger protein family and ginsenoside content,a gen-ome-wide association study of PgZFPs,and co-expression analysis of PgZFPs with validated key enzyme genes.Ultimately,five candidate genes involved in ginsenoside biosynthesis were identified.The involvement of PgZFP27 and PgZFP-59-02 genes from the PgZFPs family in the biosynthesis of ginsenosides was validated through in vitro methyl jasmonate(MeJA)induction experiments.This result provides new genetic resources for the biosynthesis of ginsenosides.
基金supported by the Programme Blanc de l’Agence National de la Recherche.
文摘Family-based tests of association between a genetic marker and a disease constitute a common design to dissect the genetic architecture of complex traits. The FBAT software is one of the most popular tools to perform such studies. However, researchers are also often interested in the genetic contribution to a more specific manifestation of the phenotype (e.g. severe vs. non-severe form) known as a secondary outcome. Here, what we demonstrate is the limited power of the classical formulation of the FBAT statistic to detect the effect of genetic variants that influence a secondary outcome, in particular when these variants also impact on the onset of the disease, the primary outcome. We prove that this loss of power is driven by an implicit hypothesis, and we propose a derivation of the original FBAT statistic, free from this implicit hypothesis. Finally, we demonstrate analytically that our new statistic is robust and more powerful than FBAT for the detection of association between a genetic variant and a secondary outcome.
基金supported by Funds of the National Key Research and Development Program(2016YFD0101006,2018YFD0100402)National Natural Science Foundation of China(31621005 and 31901581)Central Public-interest Scientific Institution Basal Research Fund(1610162021013).
文摘Background:Cotton is the source of natural fibers globally,fulfilling 90%of the textile industry’s requirements.However,fiber development is a complex biological process comprising four stages.Fiber develops from a single cell,and cell elongation is a vital process in fiber development.Therefore,it is pertinent to understand and exploit mechanisms underlying cell elongation during fiber development.A previous report about cell division control protein 42(CDC-42)with its key role in cell elongation in eukaryotes inspired us to explore its homologs Rho GTPases for understanding of cell elongation during cotton fiber development.Result:We classified 2066 Rho proteins from 8 Gossypium species into 5 and 8 groups within A and D sub-genomes,respectively.Asymmetric evolution of Rho members was observed among five tetraploids.Population fixation statistics between two short and long fiber genotypes identified highly diverged regions encompassing 34 Rho genes in G.hirustum,and 31 of them were retained through further validation by genome wide association analysis(GWAS).Moreover,a weighted gene co-expression network characterized genome-wide expression patteren of Rho genes based on previously published transcriptome data.Twenty Rho genes from five modules were identified as hub genes which were potentially related to fiber development.Interaction networks of 5 Rho genes based on transcriptional abundance and gene ontology(GO)enrichment emphasized the involvement of Rho in cell wall biosynthesis,fatty acid elongation,and other biological processes.Conclusion:Our study characterized the Rho proteins in cotton,provided insights into the cell elongation of cotton fiber and potential application in cotton fiber improvement.
