Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1212603 | ENA |
REPOSITORIES: ENA
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Project description:Pseudomonas fluorescens SBW25 cultures were inoculated into the rhizospheres of barley seedlings of the Chevallier and Tipple varieties growing in axenic cultures. Bacterial cells were collected from the rhizosphere one and five days after inculation and RNA extracted from them. Culture used for inoculation (but not exposed to the rhizospheres) were used as control. The aim of the experiment was to determine the changes in gene expression of P. fluorescens SBW25 upon exposure to barley rhizosphere and also to determine if the rhizospehres of the two varieties of Barley had different effects on gene expression of P. fluorescens SBW25.
2023-05-15 | E-MTAB-12918 | biostudies-arrayexpress
Project description:Chevallier is a heritage english landrace of barley first planted in 1820 while Tipple is modern cultivar of barley released in 2004. Pseudomonas strains were isolated from the rhizospheres of the two varieties and 22 and 20 of the most phylogenetically distinct ones were sequenced to find out the difference in genotypes preferentially selected in the rhizospheres of the two cultivars.
2023-06-15 | E-MTAB-12917 | biostudies-arrayexpress
Project description:Russeting is a commercially important defect in apple (Malus x domestica) fruit production. Apple russeting is mainly characterized by the accumulation of suberin on the inner part of the cell wall. However, knowledge on the underlying genetic components triggering this trait remains sketchy. A bulk transcriptomic profiling was performed on the exocarps of three russeted and three waxy apple varieties using RNA sequencing. This experimental design was chosen to lower the specificities of each genotype. A qPCR validation was carried out on representative genes and additional contrasting varieties. Gene ontology enrichment revealed a repression of the lignin and cuticle biosynthesis genes in the russeted exocarps, concomitantly with an enhanced expression of suberin deposition, stress responsive, primary sensing, NAC and MYB-family transcription factors, and specific triterpene biosynthetic genes. Notably, a strong correlation (R2=0.976) between the expression of a MYB93-like transcription factor and key suberin biosynthetic genes was found. Our results suggest that russeting is induced by a decreased expression of the cuticle layer biosynthetic genes, leading to a stress response which not only affects suberin deposition, but also the entire structure of the cell wall. In addition, the large number of candidate genes highlighted in this study provides a solid platform for further functional investigations. In order to draw a consistent picture of the gene expression profiles specific to both russeted and waxy apples and at the same time to highlight and interpret the mechanism leading to the russeted phenotype, a bulk RNA-sequencing was performed on the exocarp of a group of three distinct fully-russeted apple varieties ('Patte de loup', 'Reinette Parmentier', 'St Edmund's Pippin') and a second one including 3 fully waxy varieties ('Gala', 'CRAW/Ma/AF42', and 'CRAW/Ma/AG94').
2015-02-01 | E-GEOD-61040 | biostudies-arrayexpress
Project description:Drought stress, especially during the seedling stage, seriously limits the growth and development of maize. Understanding the response of maize to drought is the first step in the breeding of tolerant genotypes. Recent advances in deep-sequencing and proteomic techniques, such as isobaric tags for relative and absolute quantitation (iTRAQ), can provide large-scale comparisons and reliable quantitative measurements. Despite previous studies on drought resistance mechanisms by which maize cope with water deficient, the link between physiological and molecular variations are largely unknown. Therefore, understanding the drought tolerance mechanisms of different maize varieties is essential for genetic manipulation and/or cross breeding in maize. Towards this goal, we used a comparative physiological and proteomics analysis approach to monitor the changes of two different drought-resistant maize varieties.
2022-02-16 | PXD028508 | Pride
Project description:Transcriptomic comparison between MON810 maize embryos and near-isogenic varieties
2014-01-20 | E-MTAB-1555 | biostudies-arrayexpress
Project description:Transcriptional profiling of 4 maize varieties comparing genetic root response under control temperature conditions with genetic root response under low temperature conditions
2016-05-24 | GSE72508 | GEO
Project description:This study was conducted to follow up on apparent differences in growth, relative organ sizes, cellular stress and immune function in Atlantic salmon fed genetically modified (GM) Bt-maize compared to the non-modified parental maize line. Gene expression profiling on the distal intestinal segment and liver were performed by the cGRASP 16K salmonid cDNA microarray. Analysis of the intestinal microarray data revealed nearly 500 differentially regulated genes with a false discovery rate of zero, despite modest fold differences (average 2.4 for the down-regulated and 1.7 for the up-regulated genes). However, nine out of ten genes were found not to be significantly different when followed up by quantitative polymerase chain reaction (qPCR), but direction and magnitude of the change was generally confirmed, at least for the up-regulated genes. For the liver microarray data, statistical analyses could not be performed due to constraints in the design. qPCR revealed some differentially regulated genes in the liver, including up-regulation of gelsolin precursor, down-regulation of ferritin heavy subunit and a tendency towards down-regulation of metallothionein B. This, combined with up-regulation of anti-apoptotic protein NR13 and a tendency towards up-regulation of both ferritin heavy chain and metallothionein A and B in the distal intestine, suggests changes in cellular stress/ anti-oxidant status. This corresponds well with, and strengthens previous findings in these fish. To exclude possible confounding factors, the maize ingredients were analyzed for mycotoxins and metabolites, and the GM maize variety contain 90M-NM-<g/kg deoxynivalenol (DON), compared to levels below the detection limit in the non-GM maize. Numerous differences were also seen in the metabolite profiles of the two maize varieties, some of which seem to be connected to the mycotoxin level. The effects on salmon observed in the current and in previous studies correspond relatively well with effects of DON as reported in the literature for other production animals, but knowledge regarding effects and harmful dose levels in fish are practically non-existing, thus it is difficult to conclude whether the observed effects in the fish are caused by the DON level or by some other aspect of the GM maize ingredient.
2010-10-01 | E-TABM-1056 | biostudies-arrayexpress