Expression data from three Japonica varieties and their F1 progenies
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PROVIDER: PRJNA489242 | ENA |
REPOSITORIES: ENA
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Project description:Hybrid weakness is an important post zygotic reproductive barrier between natural populations. Expression of hybrid weakness can lead to significant decrease in yield and even lethality and is thus an undesirable agronomic trait. We observed that F1 hybrids produced from crossing between any two of three Japonica varieties(CH7, CH8, CH9) exhibit hybrid weakness phenotype. Exploring the molecular mechanism underlying hybrid weakness in important crops like rice is worthy. We used microarrays to obtain a global picture of gene expression changes that occurred in the F1 hybrids with characteristic hybrid weakness phenotype.
2018-12-01 | GSE119431 | GEO
Project description:Misgurnus anguillicaudatus breed:F1 progenies Raw sequence reads
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Project description:Plant architecture is a critical trait in fruit crops that can significantly influence yield, pruning, planting density and harvesting. Most of the existing varieties of olive are traditional and their architecture is poorly suited for modern growing and harvesting systems. This study focuses on the identification of candidate genes involved in determining plant architecture in olive that could help in selecting phenotypes adapted to modern cultivation practices. We previously developed the first microarray for olive, as a means to discover candidate genes involved in relevant agronomical traits. The microarray has already been applied to identify candidates genes involved in regulating juvenile to adult transition in the shoot apex of seedlings. In the present study, made in the framework of an olive breeding program, varieties displaying differences in architecture and pooled seedlings grouped by their architecture-related phenotypes, were analysed using microarray analysis of meristematic tissue. We identify 2,258 differentially expressed genes potentially involved in determining plant architecture. Varieties with opposite architecture phenotypes and individuals from segregating progenies displaying extreme architecture features, constitute our key to linking phenotype to expression. We analyze some of the genes with potentially interesting functional annotation using quantitative RT-PCR assays, in the reference varieties and individual seedlings. Arabidopsis mutants in putative orthologs of some of the candidate genes show altered architecture, indicating functional conservation between the two species and supporting both, the biological relevance of the results, and the potential of the identified genes as markers for assisted breeding for olive varieties suited for high density orchards.
2016-02-15 | GSE60284 | GEO
Project description:Plant architecture is a critical trait in fruit crops that can significantly influence yield, pruning, planting density and harvesting. Most of the existing varieties of olive are traditional and their architecture is poorly suited for modern growing and harvesting systems. This study focuses on the identification of candidate genes involved in determining plant architecture in olive that could help in selecting phenotypes adapted to modern cultivation practices. We previously developed the first microarray for olive, as a means to discover candidate genes involved in relevant agronomical traits. The microarray has already been applied to identify candidates genes involved in regulating juvenile to adult transition in the shoot apex of seedlings. In the present study, made in the framework of an olive breeding program, varieties displaying differences in architecture and pooled seedlings grouped by their architecture-related phenotypes, were analysed using microarray analysis of meristematic tissue. We identify 2,258 differentially expressed genes potentially involved in determining plant architecture. Varieties with opposite architecture phenotypes and individuals from segregating progenies displaying extreme architecture features, constitute our key to linking phenotype to expression. We analyze some of the genes with potentially interesting functional annotation using quantitative RT-PCR assays, in the reference varieties and individual seedlings. Arabidopsis mutants in putative orthologs of some of the candidate genes show altered architecture, indicating functional conservation between the two species and supporting both, the biological relevance of the results, and the potential of the identified genes as markers for assisted breeding for olive varieties suited for high density orchards. Active or dormant meristems to be used for expression analysis were collected from individual olive trees from four varieties Picual, Arbequina, Arbosana and Chiquitita and from seedlings of a Picual x Arbequina progeny, all of the showing variability for growth habit. Plant material was provided by the olive breeding program of Cordoba. Harvesting was carried out between 8:00 to 11:00 a.m., at the end of Spring. Samples were immediately frozen in liquid nitrogen, and maintained afterwards at -80 ºC. Samples of the Picual x Arbequina seedlings used to generate pools were harvested individually and 0.2 g of tissue per individual mixed and processed together to obtain RNA to be used for microarray analysis.
2016-02-15 | E-GEOD-60284 | biostudies-arrayexpress
Project description:RNA-sequencing for leaves of three garlic varieties
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Project description:We used a transcriptome sequencing approach to analyze different expression levels of three barley varieties under both infected and uninfected conditions
2023-05-24 | GSE225976 | GEO
Project description:By comparing mouse fibroblasts from two parental strains (Bl6 and Spretus) with fibroblasts from their first generation offspring (F1) we can detect allele specific expression of proteins. The Bl6 and Spretus lines are evolutionary distant and harbour many SNPs in their genomes which when synonomous we can detect on the protein level using mass spectrometry. By mixing SILAC labeled Bl6, Spretus and F1 offspring cell lines we can detect peptides shared between all three cell lines and also SNP peptides that are only expressed in the F1 cells and either Bl6 or Spretus cells. By comparing the abundance of the shared peptides and the SNP peptides we can quantify how much of a protein in the F1 cells that comes from the paternal or maternal allele. This data were then further compared to polysome profiling data. Azidohomoalanine labeling was used to enrich newly synthesized proteins from the three cell lines.
2015-08-18 | PXD002337 | Pride
Project description:Information about protein expression in rice grain across both pigmented and non-pigmented rice varieties is still relatively scarce. The data provided here represent proteomic data obtained from selected 6 Malaysian local rice varieties with varying pigmentations (black, red and white). The selected pigmented rice varieties such as black (BALI and Pulut hitam 9) and red rice (MRQ100 and MRM16) have shown high antioxidant activities and non-pigmented rice (MRQ76 and MR297) contain amino acid and micronutrient contents. This project aimed to obtain global protein expression profile as well as differential protein expression between the selected pigmented and non-pigmented rice varieties particularly proteins with their functions responsible for nutritional (i.e. antioxidant, folate and low glycaemic index) and quality (i.e. aromatic) traits. Integration of this proteomics dataset with other available in-house omics data could facilitate the identification of significant functional markers related to nutritional and quality traits. Total proteins were prepared from dehusked matured seeds harvested from three different rice plants of each variety (3 protein samples per variety). The proteins were trypsin digested before subjected to SWATH-MS proteomics analysis. Proteins were identified by matching tandem mass (MS/MS) spectra from both 1D and 2D IDA to Oryza sativa japonica and indica rice databases available at UniProt by using ProteinPilot software (v4.2) (AB Sciex). Quantification of proteins was carried out by determining protein peak areas extracted from SWATH analysis data sets using PeakView (v2.1) (AB Sciex) software. Differentially expressed protein between varieties were identified using T-test analysis with a set threshold for fold change ± 1.5 and p‐value < 0.05.
2020-04-27 | PXD018338 | Pride
Project description:Recent epidemiological studies suggest that hyponutritional stress during fetal period increase risks of adult-onset diseases, such as type 2 diabetes and mental diseases. Rodent models have demonstrated that hyponutrition during pregnancy alters epigenetic status of neuronal genes in the fetal brains; this implicate fatal environment contributes to susceptibility to mental disorders. However, in these studies, progenies were generated with natural mating and effects of hyponutrition during egg formation have not been eliminated. Therefore, we conducted experiments in order to finely evaluate the hyponutritional effects during fatal life using in vitro fertilization. We divided three experimental groups such as control diet (CD (AIN93G)), protein-restricted diet (PR), and PR diet with supplemental folic acid (FA) and compared body weight of mother and progenies, clinical-blood biochemistry, DNA methylation and gene-expression pattern in adult brain of the progenies, behavioral phenotypes of the progenies, and DNA methylation profile in brain of the progenies. The progenies of the PR group and the FA group exhibited increased activity in the home cage, decreased contact to a novel object, and decreased social behavior compared with the CD group. Increased home-cage activity in the PR group was rescued in the FA group. The progenies of the PR group and the FA group showed different patterns of mRNA expression and genomic methylation in the brain compared with the CD group. These results suggest that hyponutrition after insemination sufficiently induced phenotypic and epigenetic changes in the progenies. In addition, supplemental nutrition to mothers should rescue the epigenetic and phenotypic changes induced with hyponutrition.
2017-03-08 | GSE79847 | GEO
Project description:Anguilla japonica isolate:Three weekly SPH injections Transcriptome or Gene expression
| PRJNA339349 | ENA