Natural variation of gibberellin responses in Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB12877 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1295150_1.fastq.gz | Fastqsanger.gz | |||
| ERR1295150_2.fastq.gz | Fastqsanger.gz | |||
| ERR1295190_1.fastq.gz | Fastqsanger.gz | |||
| ERR1295190_2.fastq.gz | Fastqsanger.gz | |||
| ERR1295151_1.fastq.gz | Fastqsanger.gz |
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Project description:To assess natural variation in the ability to respond to changes in gibberellin metabolism, we examined the effect of the ectopic expression of GA20ox1 in 10 Arabidopsis thaliana accessions. RNA-seq was performed on the sixth leaf, which was micro-dissected (size < 0.25 mm2) at the beginning of the transition from cell proliferation to cell expansion.
2017-12-14 | E-MTAB-4508 | biostudies-arrayexpress
Project description:Natural variation within plant species is an important resource for discovery of genes controlling biological traits. Gene-expression profiling of natural variation is increasingly used to identify genes affecting a trait. Here, we explored variation among Arabidopsis thaliana accessions with respect to defense against Pseudomonas syringae pv. tomato DC3000 (Pst), with a focus on R-gene mediated resistance triggered by the Pst type III effector protein AvrRpt2. We explored variation at two phenotypic levels: growth of the bacteria and hypersensitive response (HR) measured by electrolyte leakage. Considerable variation among accessions was found at both phenotypic levels. The genetic variation among accessions affected both growth of Pst with (Pst avrRpt2) and without (Pst) the AvrRpt2 effector, with some variation being specific for the bacterial strains, and other variation affecting both strains in a similar manner. Variation in HR was not correlated with variation in bacterial growth. Additionally we examine variation in gene-expression profiles after mock- and Pst avrRpt2-inoculated plants, obtained using a dedicated microarray Gene-expression profiling at 6 h post inoculation identified clusters of genes from which expression levels are correlated with bacterial growth and electrolyte leakage. The expression levels of some of these clusters correlate with more than one phenotypic characteristic, such as growth of both Pst and Pst avrRpt2, whereas other clusters were correlated with just one biological parameter. Thus we demonstrate that variation in gene-expression profiles among Arabidopsis accessions is correlated with variation in phenotypic responses. Keywords: Comparisons of Arabidopsis thaliana accessions with respect to inoculation with Pseudomonas syringae pv tomato avrRpt2.
2007-08-09 | GSE8298 | GEO
Project description:A major effort is underway to study the natural variation within the model plant species, Arabidopsis thaliana. Much of this effort is focused on genome resequencing, however the translation of genotype to phenotype will be largely effected through variations within the transcriptomes at the sequence and expression levels. To examine the cross-talk between natural variation in genomes and transcriptomes, we have examined the transcriptomes of three divergent A. thaliana accessions using tiling arrays. Combined with genome resequencing efforts, we were able to adjust the tiling array datasets to account for polymorphisms between the accessions and therefore gain a more accurate comparison of the transcriptomes. The corrected results for the transcriptomes allowed us to correlate higher gene polymorphism with greater variation in transcript level among the accessions. Our results demonstrate the utility of combining genomic data with tiling arrays to assay non-reference accession transcriptomes.
2012-05-22 | GSE38109 | GEO
Project description:A major effort is underway to study the natural variation within the model plant species, Arabidopsis thaliana. Much of this effort is focused on genome resequencing, however the translation of genotype to phenotype will be largely effected through variations within the transcriptomes at the sequence and expression levels. To examine the cross-talk between natural variation in genomes and transcriptomes, we have examined the transcriptomes of three divergent A. thaliana accessions using tiling arrays. Combined with genome resequencing efforts, we were able to adjust the tiling array datasets to account for polymorphisms between the accessions and therefore gain a more accurate comparison of the transcriptomes. The corrected results for the transcriptomes allowed us to correlate higher gene polymorphism with greater variation in transcript level among the accessions. Our results demonstrate the utility of combining genomic data with tiling arrays to assay non-reference accession transcriptomes.
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Project description:Like protein coding genes, loci that produce microRNAs (miRNAs) are generally considered to be under purifying selection, consistent with miRNA polymorphisms being able to cause disease. Nevertheless, it has been hypothesized that variation in miRNA genes may contribute to phenotypic diversity. Here we demonstrate that a naturally occurring polymorphism in the MIR164A gene interacts epistatically with an unlinked locus to affect leaf shape and shoot architecture in Arabidopsis thaliana. A single-base pair substitution in the miRNA complementary sequence alters the stability of the miRNA:miRNA* duplex. It thereby interferes with processing of the precursor and greatly reduces miRNA accumulation. We demonstrate that this is not a rare exception, but that natural strains of Arabidopsis thaliana harbor dozens of similar polymorphisms that affect processing of a wide range of miRNA precursors. Our results suggest that natural variation in miRNA processability due to cis mutations is a common contributor to phenotypic variation in plants. sRNA sequencing transgenic A. thaliana
2012-10-31 | E-GEOD-32927 | biostudies-arrayexpress
Project description:Like protein coding genes, loci that produce microRNAs (miRNAs) are generally considered to be under purifying selection, consistent with miRNA polymorphisms being able to cause disease. Nevertheless, it has been hypothesized that variation in miRNA genes may contribute to phenotypic diversity. Here we demonstrate that a naturally occurring polymorphism in the MIR164A gene interacts epistatically with an unlinked locus to affect leaf shape and shoot architecture in Arabidopsis thaliana. A single-base pair substitution in the miRNA complementary sequence alters the stability of the miRNA:miRNA* duplex. It thereby interferes with processing of the precursor and greatly reduces miRNA accumulation. We demonstrate that this is not a rare exception, but that natural strains of Arabidopsis thaliana harbor dozens of similar polymorphisms that affect processing of a wide range of miRNA precursors. Our results suggest that natural variation in miRNA processability due to cis mutations is a common contributor to phenotypic variation in plants.
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Project description:To assess natural variation of downstream auxin responses we subjected 7 different arabidopsis ecotypes to a time course of auxin treatments. 7d-old seedlings grown in liquid culture have been treated for 0, 30 min, 1h and 3h with 1 µM IAA. Keywords: Expression profilling by array
2009-11-18 | GSE18975 | GEO
Project description:Hybrid plants and animals grow larger and more vigorously than the parents, a common phenomenon known as hybrid vigor or heterosis. Heterosis often correlates with the genetic distance between hybridizing parents, but the mechanism for this is largely unknown. We found that genetic distance was correlated with natural variation of stress responses under the control of the circadian clock. CIRCADIAN-CLOCK-ASSOCIATED1 (CCA1) and LATE-ELONGATED-HYPOCOTYL (LHY) or CCA1 alone mediate expression amplitudes and periods of these stress-responsive genes in stress and non-stress conditions. In Arabidopsis thaliana intraspecific hybrids, genome-wide expression of many biotic and abiotic stress-responsive genes was diurnally repressed to promote biomass heterosis, which is associated with several biomass quantitative trait loci (QTLs). Expression differences in four selected stress-responsive genes among ten ecotypes could be used to predict heterosis in their hybrids. Parent plants with larger expression differences between stress-responsive genes produced higher-vigor hybrids, while those with smaller differences produced lower-vigor hybrids. Stress-responsive genes were epigenetically repressed in the hybrids under normal conditions but induced during times of stress at certain times of the day, balancing the tradeoff between stress responses and growth. Consistently, repressing the stress genes in diploids increased growth vigor. We demonstrate how hybrids manipulate diurnal stress-responsive gene expression to enhance growth vigor. Both circadian and epigenetic regulation play key roles in the altered expression of stress-responsive genes in hybrids. Our findings provide a conceptual advance and mechanistic understanding of heterosis, as well as selection criteria for parents to be effectively used for producing high-yield hybrids. Examination of gene expression in Arabidopsis thaliana F1 hybrids between Col and C24 and 3 time points using mRNA-seq
2015-05-31 | E-GEOD-51578 | biostudies-arrayexpress
Project description:The aim is to identify early gibberellin responsive genes in a gibberellin deficient strain such as ga1-3. Such genes are likely regulated by DELLA proteins which are master gibberellin repressors. DELLA proteins are rapidly degraded after gibberellin treatment, but their direct target genes still need to be elucidated. Experiment Overall Design: A set of 4 biological replicates was generated for each treament. Arabidopsis seedlings were treated with water or 2 uM GA4 and whole shoots collected after 1h. A comparison of water vs. GA4 treated samples should render a list of early gibberellin responsive genes.
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Project description:This SuperSeries is composed of the following subset Series:; GSE8739: Early gibberellin responses in Arabidopsis; GSE8741: DELLA protein direct targets in Arabidopsis Experiment Overall Design: Refer to individual Series
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