Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1140178 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Twelve chili pepper accessions, six domesticated, four wild and two F1 crosses were studied. RNA-Seq experiments were performed with fruits from each accession at 7 different times after anthesis. Additionally, samples of seedlings from two accessions were evaluated. The data set is comprised by 179 samples, that in total have more than 3 billion reads map to the Capsicum annuum genome.
2021-03-16 | GSE165448 | GEO
Project description:Characterization of Genetic and Allelic Diversity Amongst Cultivated and Wild Lentil Accessions for Germplasm Enhancement
| PRJNA625627 | ENA
Project description:Gossypium barbadense is widely cultivated because of its extra-long staple cotton with superior luster, silkiness and high yield. These economically important traits were selected during initial domestication of an agronomically inferior wild ancestor, followed by millennia of human- mediated selection. To reveal the effects of this history on the cotton fiber transcriptome, we conducted comparative expression profiling on mechanically isolated fiber cells at three different stages encompassing early, mid, and late fiber elongation in wild (K101) and domesticated (Pima S-7) accessions, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes across developmental stages was different in the two accessions, with a shift toward greater change earlier in cultivated than in wild G. barbadense. Approximately 4200 genes were differentially expressed between wild and domesticated accessions at one or more of the stages studied. Domestication appears to have led to enhanced modulation of cellular redox levels and the avoidance or delay of stress-like processes. Prolonged fiber growth in cultivated relative to wild G. barbadense is associated with upregulation of signal transduction and hormone signaling genes and down-regulation of cell wall maturation genes. Clues are provided into the processes and genes that may unwittingly have been selected by humans during domestication and development of modern elite lines. Several of the transcriptomic differences between wild and domesticated G. barbadense described here appear to have parallels in a second domesticated cotton species, Gossypium hirsutum, suggesting that replicated domestication of two different species has resulted in overlapping, parallel, metabolic transformations.
2008-11-13 | GSE13022 | GEO
Project description:Cultivated soybean has domesticated in China for a long history, and there are several significant phenotypic differences between wild and cultivated soybeans. Seed of cultivar is generally larger than wild soybean, therefore here we comprehensively analyzed transcriptomes of thirteen soybean accessions seeds including seven wild soybeans and six landraces through applying strand-specific RNA sequencing. Differential expressed genes related seed weight were identified, some of them were known to be associated with seed development in Arabidopsis. Noncoding RNAs are known to play important roles in plant development, and we profiled the expression pattern of long noncoding RNA (lncRNA) in cultivated and wild soybean seeds. We have identified 1,251 long intergenic noncoding RNA, 243 intronic RNA and 81 antisense lncRNA, transcriptional levels of a number of lncRNAs were significantly different between cultivated and wild soybeans, suggesting that lncRNA may be involved in soybean seed development.
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2024-04-28 | GSE264132 | 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. 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: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:Background
Specialized metabolism plays a crucial role in plant interactions with biotic and abiotic environments, and its characterization in crops is an essential objective for optimizing ecosystem services in breeding programs. However, our knowledge of specialized metabolism in cultivated Brassica species remains insufficient to fully support these breeding strategies.
Results
In this study, we conducted a detailed exploration of both constitutive and stress-induced specialized metabolites in response to CuCl2 in the leaves and roots of 20 Brassica rapa and B. oleracea accessions using UHPLC-HRMS/MS-based untargeted metabolomics. Our analysis revealed a wide range of species-specific chemical signatures and allowed the putative annotation of nearly 200 compounds belonging to various chemical families, including flavonoids, glucosinolates, phenolamides, indoles, amino acids, oxylipins and coumarins. A detailed interpretation of ion fragmentation patterns uncovered both inter- and intra-specific structural variations within these chemical families, providing deeper insights into the phytochemical diversity of B. rapa and B. oleracea species. This study also enabled the identification of previously unreported compounds in these species, including the carotenoid-derivatives blumenols, flavonols decorated with rhamnoside moieties or pentahexosylated flavonols. Finally, we showed that these resources, combined with the high-quality genetic data available for these accessions, allowed the identification of genetic variants of MAM2 genes possibly involved in the control of 4C or 3C/4C-aliphatic glucosinolate chemotypes among B. oleracea accessions.
Conclusions
This work thus lays the foundation for future studies on functional genomics of specialised metabolism in Brassica species in a chemical ecology perspective, and aiming to harness metabolic diversity in breeding programs.
2026-01-08 | MSV000100402 | MassIVE