Ontology highlight
ABSTRACT:
PROVIDER: PRJNA926123 | ENA |
REPOSITORIES: ENA
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Project description:There is growing evidence for the prevalence of DNA copy number variation (CNV) and its role in phenotypic variation in recent years. Comparative genomic hybridization (CGH) was used to explore the extent of this type of structural variation in the barley genome. In a panel of 14 genotypes including domesticated cultivars and wild barleys, we found that 14.9% of all the sequences on the array are affected by CNV. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. A substantial portion (37%) of the CNV events are present in both wild and domesticated barley. CNVs are enriched in telomeric regions for all chromosomes except 4H, which is also the barley chromosome with the lowest proportion of CNVs. CNV affected 9.5% of the coding sequences represented on the array. The genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases, suggesting the potential for CNV to influence variation for responses to biotic and abiotic stress. The analysis of CNV breakpoints indicated that DNA repair mechanisms of double-strand breaks (DSBs) via single-stranded annealing (SSA) and synthesis-dependent strand annealing (SDSA) play an important role in the origin of many structural changes in barley. Here we present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. 1-2 replications of 8 barley cultivars and 6 wild barley accessions were hybridized to an array designed from 115,003 whole genome shotgun (WGS) contigs of the ‘reference’ genome of cv. Morex
2013-05-09 | E-GEOD-44293 | biostudies-arrayexpress
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
Project description:We have collected RNA-seq data from the total RNA isolated from the 2-week seedlings of 198 diverse wheat accessions. These accessions were selected among nearly 3,000 lines to represent the broad geographic and genetic diversity of wheat populations. On average, 65.7 million paired-end Illumina reads (2 x 100 bp) were collected for each sample, and after quality trimming were mapped to the wheat reference genome RefSeq v.1.0. The proportion of reads unambiguously mapped to the individual wheat genomes was 81%, with the accuracy of correct read mapping estimated by simulation achieving 98%. The expression levels measured as Transcripts Per Million (TPM) were estimated for high confidence (HC) gene models in the wheat reference genome, with 82,092 gene models (66,333 genes) showing TPM > 0.5 in at least two wheat lines (PRJNA670223)
2022-01-17 | GSE167479 | GEO
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. MethylC-seq from naturally-occurring Arabidopsis accessions
2013-03-05 | E-GEOD-43857 | biostudies-arrayexpress
Project description:Copy number variations (CNVs) can create new genes, change gene dosage, reshape gene structures, and modify elements regulating gene expression. As with all types of genetic variation, CNVs may influence phenotypic variation and gene expression. CNVs are thus considered major sources of genetic variation. Little is known, however, about their contribution to genetic variation in rice. To detect CNVs, we used a set of NimbleGen whole-genome comparative genomic hybridization arrays containing 715,851 oligonucleotide probes with a median probe spacing of 500 bp. We compiled a high-resolution map of CNVs in the rice genome, showing 641 CNVs between the genomes of the rice cultivars ‘Nipponbare’ (from O. sativa ssp. japonica) and ‘Guang-lu-ai 4’ (from O. sativa ssp. indica). These CNVs contain some known genes. They are linked to variation among rice varieties, and are likely to contribute to subspecific characteristics.
2012-07-01 | GSE30542 | GEO
Project description:These data provide a basis for exploration of gene expression differences between physiologically diverse accessions of Arabidopsis thaliana. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. Therefore we studied the physiology, genome content and gene expression of 18 physiologically diverse accessions. The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit.
2012-03-12 | GSE27550 | GEO
Project description:These data provide a basis for exploration of gene expression differences between physiologically diverse Spring annual accessions of Arabidopsis thaliana. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. Therefore we studied the physiology, genome content and gene expression of 18 physiologically diverse accessions. The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit.
2012-03-12 | GSE27548 | GEO
Project description:These data provide a basis for the detection of sequence based polymorphisms between 10 Spring annual accessions of Arabidopsis thaliana. The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit.
2012-03-12 | GSE27551 | GEO