Genetic variation and gene expression of anthocyanin synthesis and transport related enzymes in Oryza sativa against thiocyanate

Anthocyanins are vital components of plant secondary metabolites, and are also the most important coloring substances in wine. Teinturier cultivars are rich in anthocyanins. However, the differences in anthocyanin accumulation and profiles between teinturier and non-teinturier cultivars have not been reported. In this study, Yan 73 and Dunkelfelder were selected as the experimental materials, and three non-teinturier cultivars were used for comparison. LC-MS and qRT-PCR were used to determine the individual anthocyanin contents and the relative gene expression. The results show that the total anthocyanin content of the teinturier cultivars was considerably higher than that in non-teinturier cultivars, and the levels of individual anthocyanins increased gradually during ripening. Lower ratios of modified anthocyanins were found in the teinturier cultivars, which was not only due to the high expression level of VvUFGT and VvGST4, but also due to the relatively low expression of VvOMT in these cultivars. Cluster analysis of gene expression and anthocyanin accumulation showed that VvUFGT is related to anthocyanin accumulation, and that AM1 is related to the synthesis and transport of methylated anthocyanins. Our results will be useful for further clarifying the pathways of anthocyanin synthesis, modification, and transport in teinturier cultivars.

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Study on a class of genetic variation algorithm in gene expression

2017 Chinese Automation Congress (CAC) ◽

10.1109/cac.2017.8243885 ◽

2017 ◽

Author(s):

Yuqing Zhao ◽

Rui Gao ◽

Guiying Dong

Keyword(s):

Gene Expression ◽

Genetic Variation

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Collaborative Cross Founder Expression Analysis (CCFEA)

10.1101/2021.03.04.422591 ◽

2021 ◽

Author(s):

Richard R Green ◽

Renee C Ireton ◽

Martin Ferris ◽

Kathleen Muenzen ◽

David R Crosslin ◽

...

Keyword(s):

Gene Expression ◽

Genetic Variation ◽

Gene Expression Data ◽

Viral Infections ◽

Collaborative Cross ◽

Visualization Tool ◽

Expression Data ◽

Individual Gene ◽

Rnaseq Data

To understand the role of genetic variation in SARS and Influenza infections we developed CCFEA, a shiny visualization tool using public RNAseq data from the collaborative cross (CC) founder strains (A/J, C57BL/6J, 129s1/SvImJ, NOD/ShILtJ, NZO/HILtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ). Individual gene expression data is displayed across founders, viral infections and days post infection.

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Loci, genes, and gene networks associated with life history variation in a model ecological organism,Daphnia pulex(complex)

10.1101/436733 ◽

2018 ◽

Author(s):

Jacob W. Malcom ◽

Thomas E. Juenger ◽

Mathew A. Leibold

Keyword(s):

Gene Expression ◽

Genetic Variation ◽

Life History ◽

Molecular Basis ◽

Life History Traits ◽

Evolutionary Dynamics ◽

Daphnia Pulex ◽

Life History Trait ◽

Life History Variation ◽

Trait Variation

ABSTRACTBackgroundIdentifying the molecular basis of heritable variation provides insight into the underlying mechanisms generating phenotypic variation and the evolutionary history of organismal traits. Life history trait variation is of central importance to ecological and evolutionary dynamics, and contemporary genomic tools permit studies of the basis of this variation in non-genetic model organisms. We used high density genotyping, RNA-Seq gene expression assays, and detailed phenotyping of fourteen ecologically important life history traits in a wild-caught panel of 32Daphnia pulexclones to explore the molecular basis of trait variation in a model ecological species.ResultsWe found extensive phenotypic and a range of heritable genetic variation (~0 < H2< 0.44) in the panel, and accordingly identify 75-261 genes—organized in 3-6 coexpression modules—associated with genetic variation in each trait. The trait-related coexpression modules possess well-supported promoter motifs, and in conjunction with marker variation at trans- loci, suggest a relatively small number of important expression regulators. We further identify a candidate genetic network with SNPs in eight known transcriptional regulators, and dozens of differentially expressed genes, associated with life history variation. The gene-trait associations include numerous un-annotated genes, but also support several a priori hypotheses, including an ecdysone-induced protein and several Gene Ontology pathways.ConclusionThe genetic and gene expression architecture ofDaphnialife history traits is complex, and our results provide numerous candidate loci, genes, and coexpression modules to be tested as the molecular mechanisms that underlieDaphniaeco-evolutionary dynamics.

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Population-scale long-read sequencing uncovers transposable elements contributing to gene expression variation and associated with adaptive signatures in Drosophila melanogaster

10.1101/2021.10.08.463646 ◽

2021 ◽

Author(s):

Gabriel Rech ◽

Santiago Radio ◽

Sara Guirao-Rico ◽

Laura Aguilera ◽

Vivien Horvath ◽

...

Keyword(s):

Gene Expression ◽

Genetic Variation ◽

Transposable Elements ◽

Natural Populations ◽

Gene Expression Variation ◽

High Quality ◽

Expression Variation ◽

Climatic Regions ◽

Genomic Studies ◽

Reference Genomes

High quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generated 32 high-quality reference genomes for the well-known model species D. melanogaster and focused on the identification and analysis of transposable element variation as they are the most common type of structural variant. We showed that integrating the genetic variation across natural populations from five climatic regions increases the number of detected insertions by 58%. Moreover, 26% to 57% of the insertions identified using long-reads were missed by short-reads methods. We also identified hundreds of transposable elements associated with gene expression variation and new TE variants likely to contribute to adaptive evolution in this species. Our results highlight the importance of incorporating the genetic variation present in natural populations to genomic studies, which is essential if we are to understand how genomes function and evolve.

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The Assessment of Genetic Variation of Rice (Oryza Sativa L.) Recombinant Lines Based On Some of Quantitative and Qualitative Traits

Journal of Crop Breeding ◽

10.29252/jcb.10.26.166 ◽

2018 ◽

Vol 10 (26) ◽

pp. 166-172

Author(s):

Mohammad Ali Ahmadi Shad ◽

Ali Akbar Ebadi ◽

Mohammad Mehdi Sohani ◽

Habibollahe Samizadh Lahiji ◽

Maryam Hosseini Chaleshtori ◽

...

Keyword(s):

Genetic Variation ◽

Oryza Sativa ◽

Oryza Sativa L ◽

Qualitative Traits ◽

Quantitative And Qualitative Traits

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Leveraging DNA methylation quantitative trait loci to characterize the relationship between methylomic variation, gene expression and complex traits

10.1101/297176 ◽

2018 ◽

Author(s):

Eilis Hannon ◽

Tyler J Gorrie-Stone ◽

Melissa C Smart ◽

Joe Burrage ◽

Amanda Hughes ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Genetic Variation ◽

Quantitative Trait Loci ◽

Quantitative Trait ◽

Complex Traits ◽

Common Genetic Variation ◽

Online Data ◽

The Relationship ◽

Methylation Quantitative Trait Loci

ABSTRACTCharacterizing the complex relationship between genetic, epigenetic and transcriptomic variation has the potential to increase understanding about the mechanisms underpinning health and disease phenotypes. In this study, we describe the most comprehensive analysis of common genetic variation on DNA methylation (DNAm) to date, using the Illumina EPIC array to profile samples from the UK Household Longitudinal study. We identified 12,689,548 significant DNA methylation quantitative trait loci (mQTL) associations (P < 6.52x10-14) occurring between 2,907,234 genetic variants and 93,268 DNAm sites, including a large number not identified using previous DNAm-profiling methods. We demonstrate the utility of these data for interpreting the functional consequences of common genetic variation associated with > 60 human traits, using Summary data–based Mendelian Randomization (SMR) to identify 1,662 pleiotropic associations between 36 complex traits and 1,246 DNAm sites. We also use SMR to characterize the relationship between DNAm and gene expression, identifying 6,798 pleiotropic associations between 5,420 DNAm sites and the transcription of 1,702 genes. Our mQTL database and SMR results are available via a searchable online database (http://www.epigenomicslab.com/online-data-resources/) as a resource to the research community.

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Genome-wide H3K9 Acetylation Level Increases with Age-Dependent Senescence of Flag Leaf in Rice (Oryza sativa)

10.1101/2021.11.14.468555 ◽

2021 ◽

Author(s):

Yu Zhang ◽

Yanyun Li ◽

Yuanyuan Zhang ◽

Zeyu Zhang ◽

Deyu Zhang ◽

...

Keyword(s):

Gene Expression ◽

Oryza Sativa ◽

Leaf Senescence ◽

Epigenetic Modification ◽

Flag Leaf ◽

Regulation Of Gene Expression ◽

Leaf Aging ◽

Genome Wide ◽

Age Dependent ◽

H3k9 Acetylation

Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and epigenetic modification, but the precise mechanism is as of yet unclear. Here, we analyzed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq) and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac and gene expression and transcript elongation. A set of 1,249 up-regulated, differentially expressed genes (DEGs) and 996 down-regulated DEGs showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac was observed during rice flag leaf aging. We produced a landscape of H3K9 acetylation- modified gene expression targets that includes known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis- related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac and also elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.

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