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Natural variation in Arabidopsis thaliana transcriptomes

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE24669 | GEO | 2012/03/12

SECONDARY ACCESSION(S): PRJNA132277

REPOSITORIES: GEO

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Natural variation in Arabidopsis thaliana transcriptomes

2012-05-22 | GSE38109 | GEO

Natural variation in Arabidopsis thaliana transcriptomes

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. Wild type accessions Col-0, Bur-0 and C24 were grown on soil at 23M-BM-0C with a 16 hour light period. Inflorescence tissue up to floral stage 14 was used for RNA extraction. Samples were collected 7-8 hours into the light period, with tissue from five plants pooled for each sample. RNA samples were converted into double stranded and hybridized to whole genome tiling arrays (Affymetrix Arabidopis Tiling1.0RM-BM-.). Three biological replicates were performed for each accession.

2012-03-12 | E-GEOD-24669 | biostudies-arrayexpress

Natural variation in Arabidopsis thaliana transcriptomes

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. Wild type accessions Col-0 were grown on soil at 16M-BM-0C with a 16 hour light period. Inflorescence tissue up to floral stage 14 was used for RNA extraction. Samples were collected 7-8 hours into the light period, with tissue from five plants pooled for each sample. RNA samples were converted into double stranded and hybridized to whole genome tiling arrays (Affymetrix Arabidopis Tiling1.0RM-BM-.). Three biological replicates were performed for each accession.

2012-05-21 | E-GEOD-38109 | biostudies-arrayexpress

Natural variation in RPS2-mediated resistance: correlating gene-expression profiles to phenotypic responses.

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

eXtreme Array Mapping (XAM) for the low leaf Cd phenotype in Arabidopsis thaliana accession CS28181

Project description:Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5 M-bM-^@M-^S 2 M-NM-<g Cd g-1 dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. By combining genome-wide association mapping, linkage mapping in an experimental F2 population and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions. Analysis of the predicted amino acid sequence of HMA3 from 149 A. thaliana accessions reveals the existence of 10 major natural protein haplotypes. Association of these haplotypes with leaf Cd accumulation and genetics complementation experiments indicate that 5 of these haplotypes are active and 5 are inactive, and that elevated leaf Cd accumulation is associated with the reduced function of HMA3 caused by a nonsense mutation and polymorphisms that change two specific amino acids. Genomic DNA from two F2 progeny pools (low leaf Cd pool and high leaf Cd pool) of CS28181 x Col-0 was labelled and hybridized separately to the Affymetrix SNP-tiling array AtSNPtile. The signal intensity difference between the two pools for all probes were analyzed using R scripts that are available at http://ars.usda.gov/mwa/bsasnp .

2012-07-30 | E-GEOD-39679 | biostudies-arrayexpress

eXtreme Array Mapping (XAM) for the low leaf Cd phenotype in Arabidopsis thaliana accession CS28181

Project description:Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5 – 2 μg Cd g-1 dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. By combining genome-wide association mapping, linkage mapping in an experimental F2 population and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions. Analysis of the predicted amino acid sequence of HMA3 from 149 A. thaliana accessions reveals the existence of 10 major natural protein haplotypes. Association of these haplotypes with leaf Cd accumulation and genetics complementation experiments indicate that 5 of these haplotypes are active and 5 are inactive, and that elevated leaf Cd accumulation is associated with the reduced function of HMA3 caused by a nonsense mutation and polymorphisms that change two specific amino acids.

2012-07-31 | GSE39679 | GEO

Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (RNA-Seq)

Project description:Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation. Here, we report population-wide DNA sequencing of genomes, transcriptomes, and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are unlinked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified 2,372 methylQTL, which revealed the first population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically reactivated during male gametogenesis, which facilitates their silencing across generations. RNA-seq from naturally-occurring Arabidopsis accessions

2013-03-05 | E-GEOD-43858 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:Natural variation in Arabidopsis thaliana transcriptomes

| PRJNA167306 | ENA

Arabidopsis thaliana

Project description:Natural variation in Arabidopsis thaliana transcriptomes

| PRJNA132277 | ENA

Transcriptional response to UV treatment in several Arabidopsis thaliana accessions

Project description:UV radiation is a ubiquitous component of solar radiation that affects plant growth and development. Analysis of natural variation in response to UV radiation revealed significant differences among natural accessions of Arabidopsis thaliana. However, the genetic basis of this is to a large extent unknown. Here, we analyzed the response of Arabidopsis accessions to UV radiation stress by performing RNA-sequencing of three UV sensitive and three UV resistant accessions. The genome-wide transcriptional analysis revealed a large number of genes significantly up- or down-regulated only in sensitive or only in resistant accessions, respectively. Mutant analysis of few selected candidate genes suggested by the RNA-sequencing results indicate a connection between UV radiation stress and plant-pathogen-like defense responses.

2015-01-13 | GSE64870 | GEO

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