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Rfppr-Comparing nuclear gene expression in two CMS-systems using microarray technology

ABSTRACT: ra05-11_cmsrapeseed - rfppr - -To understand how/if fertility and the mitochondrial background are interlinked. -To understand how the mitochondrial background influences the nuclear gene expression. -Compare and describe the total nuclear gene expression of CMS vs. fertile and CMS vs. Restored. -Describe and analyse genes that differ in expression (of special interest are genes that differs in both comparisons). -Group genes e.g. floral genes, highly expressed genes, transcription factors, nuclear encoded genes targeted for the mitochondrion. -Comparing two CMS-systems to elucidate differences and similarities between them. - Flower buds from three B. napus lines (Pactol, CMS, Rfo PPR) at one developmental stage (stage 8). Keywords: wt vs mutant comparison

ORGANISM(S): Arabidopsis thaliana Brassica napus

PROVIDER: GSE8820 | GEO | 2008/08/01

SECONDARY ACCESSION(S): PRJNA102141

REPOSITORIES: GEO

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rfppr-Comparing nuclear gene expression in two CMS-systems using microarray technology

Project description:ra05-11_cmsrapeseed - rfppr - -To understand how/if fertility and the mitochondrial background are interlinked. -To understand how the mitochondrial background influences the nuclear gene expression. -Compare and describe the total nuclear gene expression of CMS vs. fertile and CMS vs. Restored. -Describe and analyse genes that differ in expression (of special interest are genes that differs in both comparisons). -Group genes e.g. floral genes, highly expressed genes, transcription factors, nuclear encoded genes targeted for the mitochondrion. -Comparing two CMS-systems to elucidate differences and similarities between them. - Flower buds from three B. napus lines (Pactol, CMS, Rfo PPR) at one developmental stage (stage 8). Keywords: wt vs mutant comparison 6 dye-swap - CATMA arrays

2008-07-31 | E-GEOD-8820 | biostudies-arrayexpress

cms4:19 and at chr3-Comparing nuclear gene expression in two CMS-systems using microarray technology

Project description:ra05-11_cmsrapeseed - cms4:19 and at chr3 - -To understand how/if fertility and the mitochondrial background are interlinked. -To understand how the mitochondrial background influences the nuclear gene expression. -Compare and describe the total nuclear gene expression of CMS vs. fertile and CMS vs. Restored. -Describe and analyse genes that differ in expression (of special interest are genes that differs in both comparisons). -Group genes e.g. floral genes, highly expressed genes, transcription factors, nuclear encoded genes targeted for the mitochondrion. -Comparing two CMS-systems to elucidate differences and similarities between them. - Flower buds from four different B. napus lines (fertile cv Hanna, CMS-line 4:19, restored line 46, cv Hanna with the additon of A. thaliana chr 3) at two developmental stages (stages 0-5 and stage 8). Keywords: wt vs mutant comparison 16 dye-swap - CATMA arrays

2008-07-31 | E-GEOD-8819 | biostudies-arrayexpress

cms4:19 and at chr3-Comparing nuclear gene expression in two CMS-systems using microarray technology

2008-08-01 | GSE8819 | GEO

The radish Ogura fertility restorer impedes translation elongation along its cognate CMS-causing mRNA

Project description:The control of mRNA translation has been increasingly recognized as a key regulatory step for gene control but clear examples in eukaryotes are still scarce. Nucleo-cytoplasmic male sterilities (CMS) represent ideal genetic models to dissect genetic interactions between the mitochondria and the nucleus in plants. This trait is determined by specific mitochondrial genes and is associated with a pollen sterility phenotype that can be suppressed by nuclear genes known as restorer-of-fertility (Rf) genes. In the study, we focused on the Ogura CMS system in rapeseed and showed that the suppression to male sterility by the PPR-B fertility restorer (also called Rfo) occurs through a specific inhibition of the translation of the mitochondria-encoded cms-causing mRNA orf138. We also demonstrate that PPR-B binds within the coding sequence of orf138 and acts as a ribosome blocker to specifically impede translation elongation along the orf138 mRNA. Rfo is the first recognized fertility restorer shown to act this way. These observations will certainly facilitate the development of synthetic fertility restorers for CMS systems in which efficient natural Rfs are lacking.

2021-10-01 | GSE178543 | GEO

The radish Ogura fertility restorer impedes translation elongation along its cognate CMS-causing mRNA [RNA-seq]

2021-10-01 | GSE178722 | GEO

stifenia-Effects of Stifenia pretreatment on Arabidopsis thaliana resistance against Fusarium oxysporum pv rafani

Project description:ra05-07_stifenia - stifenia - Does Stifenia elicitor pretreatment prime defense genes? - Stifenia sprayed and/or Fusarium infection. Keywords: treated vs untreated comparison

2008-03-12 | GSE10713 | GEO

Dnmt3a KO CMS-Seq

Project description:Dnmt3a KO vs. WT CMS-Seq in 129S4/SvJae background

2018-05-16 | GSE100952 | GEO

Transcriptome Sequencing and De Novo Analysis of a Cytoplasmic Male Sterile Line and Its Near-Isogenic Restorer Line in Chili Pepper (Capsicum annuum L.)

Project description:Background: The use of cytoplasmic male sterility (CMS) in F1 hybrid seed production of chili pepper is increasingly popular. However, the molecular mechanisms of cytoplasmic male sterility and fertility restoration remain poorly understood due to limited transcriptomic and genomic data. Therefore, we analyzed the difference between a CMS line 121A and its near-isogenic restorer line 121C in transcriptome level using next generation sequencing technology (NGS), aiming to find out critical genes and pathways associated with the male sterility. Results: We generated approximately 53 million sequencing reads and assembled de novo, yielding 85,144 high quality unigenes with an average length of 643 bp. Among these unigenes, 27,191 were identified as putative homologs of annotated sequences in the public protein databases, 4,326 and 7,061 unigenes were found to be highly abundant in lines 121A and 121C, respectively. Many of the differentially expressed unigenes represent a set of potential candidate genes associated with the formation or abortion of pollen. Conclusions: Our study profiled anther transcriptomes of a chili pepper CMS line and its restorer line. The results shed the lights on the occurrence and recovery of the disturbances in nuclear-mitochondrial interaction and provide clues for further investigations. Anther transcriptomes of a chili pepper CMS line 121A and its nearisogenic restorer line 121C were generated by deep sequencing, using Illumina HiSeq 2000.

2013-07-03 | E-GEOD-45431 | biostudies-arrayexpress

erwinia-Regulation of the Arabidopsis transcriptome by the type three secretion system (TTSS) of Erwinia amylovora

Project description:ra05-02_erwinia - erwinia - Identification of Arabidopsis genes regulataed by Erwinia amylovora and of a subset of Arabiddopsis genes regulated by the type three secretion system of Erwinia amylovora. Keywords: normal vs disease comparison

2007-08-09 | GSE8701 | GEO

MitoExome Sequencing of Mitochondrial OXPHOS Diseases (MGH)

Project description: Human disorders of mitochondrial oxidative phosphorylation (OXPHOS) represent a devastating collection of inherited diseases. These disorders impact at least 1:5000 live births, and are characterized by multi-organ system involvement. They are characterized by remarkable locus heterogeneity, with mutations in the mtDNA as well as in over 77 nuclear genes identified to date. It is estimated that additional genes may be mutated in these disorders. To discover the genetic causes of mitochondrial OXPHOS diseases, we performed targeted, deep sequencing of the entire mitochondrial genome (mtDNA) and the coding exons of over 1000 nuclear genes encoding the mitochondrial proteome. We applied this 'MitoExome' sequencing to 124 unrelated patients with a wide range of OXPHOS disease presentations from the Massachusetts General Hospital Mitochondrial Disorders Clinic. The 2.3Mb targeted region was captured by hybrid selection and Illumina sequenced with paired 76bp reads. The total set of 1605 targeted nuclear genes included 1013 genes with strong evidence of mitochondrial localization from the MitoCarta database, 377 genes with weaker evidence of mitochondrial localization from the MitoP2 database and other sources, and 215 genes known to cause other inborn errors of metabolism. Approximately 88% of targeted bases were well-covered (>20X), with mean 200X coverage per targeted base.

| phs000339 | dbGaP

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