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Ethylene and 1-MCP differentially regulate gene expression during onion (Allium cepa L.) sprout suppression

ABSTRACT: Onion is regarded as non-climacteric. In onion, ethylene can suppress sprouting however, the ethylene binding inhibitor, 1-MCP can also suppress sprout growth although it is unknown how ethylene and 1-MCP elicit the same response. In this study, onion bulbs were treated with 10 μL L-1 ethylene or 1 μL L-1 1-MCP individually or in combination for 24 h at 20°C before or after curing (six weeks) at 20 or 28°C then stored at 1°C. Following curing, a subset of these same onion bulbs was stored separately under continuous air or ethylene (10 μL L-1) at 1°C

ORGANISM(S): Allium cepa

PROVIDER: GSE27132 | GEO | 2011/06/29

SECONDARY ACCESSION(S): PRJNA137651

REPOSITORIES: GEO

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Ethylene and 1-MCP differentially regulate gene expression during onion (Allium cepa L.) sprout suppression

Project description:Onion is regarded as non-climacteric. In onion, ethylene can suppress sprouting however, the ethylene binding inhibitor, 1-MCP can also suppress sprout growth although it is unknown how ethylene and 1-MCP elicit the same response. In this study, onion bulbs were treated with 10 μL L-1 ethylene or 1 μL L-1 1-MCP individually or in combination for 24 h at 20°C before or after curing (six weeks) at 20 or 28°C then stored at 1°C. Following curing, a subset of these same onion bulbs was stored separately under continuous air or ethylene (10 μL L-1) at 1°C Six treatments were chosen for microarray analysis; four samples were taken before curing immediately after treatment with ethylene or 1-MCP or ethylene and 1-MCP in combination for 24 h at 20°C. The other two samples and two were taken at the end of storage following 6 weeks curing at 28°C andafter 29 weeks cold storage (1°C) in continuous air or continuous ethylene totalling 35 weeks storage. The four pre-curing samples used were untreated (control) or treated with EB, MB or EMB and the two samples after storage were control bulbs stored in continuous ethylene or air at 1°C. There were three biological replicates of each of the six treatments making 18 samples in total.

2011-06-29 | E-GEOD-27132 | biostudies-arrayexpress

Physiological, biochemical and transcriptional analysis of onion bulbs during storage

Project description:Physiological and biochemical changes occur in onion (Allium cepa L.) bulbs during the transition from dormancy to sprout suppression and subsequent sprout growth. These include changes in the concentrations of flavor compounds, carbohydrates, mineral elements and plant growth regulators (PGRs). Detailed analyses of these changes and the impact of different post-harvest techniques, designed to prolong storage life, have not been undertaken. We developed the first onion oligonucleotide microarray to determine differential gene expression in onion during curing and storage, with transcriptional changes supporting biochemical and physiological analyses. Samples of RNA were prepared from onions of two cultivars, ‘Wellington’ (brown, long-storing) and ‘Sherpa’ (brown, average-storing), grown according to normal commercial practice at various physiological ages, viz, freshly harvested, cured, pre-sprouting and sprouting. Three biological replicates for each time (harvest, cured, before sprouting, sprouting), curing temperature (20, 28°C) and cultivar (Wellington, Sherpa) combination (n = 42).

2012-01-15 | E-GEOD-28159 | biostudies-arrayexpress

Physiological, biochemical and transcriptional analysis of onion bulbs during storage

2012-01-15 | GSE28159 | GEO

RNA-Sequencing of onion bulbs inoculated with Salmonella

Project description:The goal of this study was to compare differentially expressed transcripts in onion bulbs induced when inoculated with Salmonella using transcriptome profiling (RNA-seq) .Transcriptomic analysis of onion bulb tissue (Variety Don Victor) in response to Salmonella was performed 24 hours and 7 days post-inoculation to identify Differentially Expressed Genes (DEGs) in onion. Within 24 hours of inoculation, 4259 genes were upregulated while 3393 genes were downregulated. After 7 days, 8213 and 6417 genes were up and down-regulated, respectively, as shown below. (FDR<0.05 and Abs (log 2(Y/X) >0)

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RNA-Sequencing of Salmonella species inoculated in onion bulb tissue

Project description:This study aimed to compare differentially expressed transcripts in Salmonella recovered from the inoculated onion bulbs using transcriptome profiling (RNA-seq). The Salmonella strains of Salmonella enterica subsp. enterica ser. Newport, isolated from clinical cases affected by the onion-linked outbreak in 2020 (CDC, 2020), was used for the onion bulb inoculation. Transcriptomic analysis of Salmonella was performed 1 day (24 hours) and 7 days post-inoculation to identify Differentially Expressed Genes (DEGs) . 925 and 736 genes were upregulated within 24 hours and seven days after inoculation, while the number of downregulated genes in the same timeframe was 690 and 826, respectively (FDR<0.05 and Abs (log 2(Y/X) >0).

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RNA-Sequencing of onion bulbs exposed to managed stress

Project description:The goal of this study was to compare differentially expressed transcripts in onion bulbs induced in response to managed stress under field conditions using transcriptome profiling (RNA-seq). The clean reads were aligned to the reference genome (a doubled haploid onion line DHCU066619 (https://www.oniongenome.wur.nl/) and the transcriptions assembly. The read count for every transcript was determined from the findings of the mapping process. Genes identified as differentially expressed genes (DEGs) had an adjusted P-value <0.05 and an absolute log2FC ≥0, as determined by DESeq2. Transcriptomic analysis of onion bulb tissue (variety Matahari) in response to nitrogen stress under optimal water identified 3092 and 2204 Differentially Expressed Genes (DEGs) unique genes under optimal nitrogen vs low nitrogen. while under sub-optimal nitrogen, 2770 and 2198 unique genes were identified under optimal nitrogen vs low nitrogen respectively.

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Effect of 1-methylcyclopropene (1-MCP) on preclimacteric nectarine (Prunus persica cv Stark Red Gold) fruit.

Project description:Peach is a climacteric fruit whose ripening is largely dependent on ethylene. Recently, it has been shown that auxin is able to autonomously regulate the expression of ripening related genes, and that a cross-talk between ethylene and auxin occurs during the ripening process. By using the non-destructing index of absorbance difference (IAD), mature nectarines were homogeneously grouped into three classes (0, 1 and 2) according to their ripening phase and treated with 1-methylcyclopropene (1-MCP), known to block ethylene receptors. 1-MCP responses differed in the three classes that were thus used to molecularly investigate the auxin-ethylene cross-talk during the transition from maturation to ripening and the accompanying switch of ethylene biosynthesis from System-1 to System-2. Microarray experiments showed that 1-MCP modified the expression of 121 genes (63 were up-regulated and 59 down-regulated). Besides inducing ethylene-, auxin- and ripening-repressed genes and repressing ethylene-, auxin- and ripening-induced genes, also genes induced by ripening, auxin and 1-MCP were discovered. The up-regulating effect of 1-MCP was observed for ctg134, similar to signalling peptides, for 1-aminocyclopropane-1-carboxylic acid synthase 1 (ACS1) and, interestingly, for many auxin-regulated genes, such as GH3, whose expression is widely used as a marker for free auxin. The latter finding, together with the induction of an IAA amidohydrolase, suggests that the 1-MCP application could have caused a rise in free auxin, thus leading to an increase in ethylene biosynthesis through the induction of the tightly regulated ACS1 gene.

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RNA-Sequencing of onion bulbs inoculated with Salmonella

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Onion Transcriptome assembly

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