Maize ear microbione
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB37077 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3974610.fastq.gz | Fastqsanger.gz | |||
| ERR3974620.fastq.gz | Fastqsanger.gz | |||
| ERR3974630.fastq.gz | Fastqsanger.gz | |||
| ERR3974640.fastq.gz | Fastqsanger.gz | |||
| ERR3974650.fastq.gz | Fastqsanger.gz |
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Project description:An gene-expression comparison of the wild type and strain delta-fst1 of Fusarium verticillioides grown on autoclaved maize kernels for six days was conducted. Comparison of gene-expression between the wild type and strain delta-fst1 of Fusarium verticillioides grown on autoclaved maize kernels for six days. For each strain, RNA was isolated from four biological replicates. Sequences was obtain by HiSeq Illumina sequencer.
2015-02-19 | E-GEOD-66044 | biostudies-arrayexpress
Project description:Fusarium verticillioides is a detrimental fungus that can contaminate maize grains with mycotoxins that are harmful to human and animal health. Breeding and growing resistant genotypes is one alternative to reduce contamination and subsequent production of mycotoxins by this fungus. However, little is known about the resistant mechanism relevant to breeding in this pathosystem. Therefore, our aim was to identify genes and metabolites that may be related to Fusarium ear rot resistance using resistant and susceptible maize inbreds. Kernels of the resistant inbred showed significantly reduced disease severity, and reduced levels of total fumonisin and ergosterol content compared with the susceptible one. Gene expression data were obtained from microarray hybridizations using F. verticillioides inoculated and non inoculated maize kernels. Differentially expressed sequences were identified and classified into 36 functional categories. Most of the differentially expressed genes were assigned to the categories “protein, RNA, DNA, stress, transport, signaling and cell metabolism”. These genes encode for PR proteins, detoxification and primary metabolism enzymes. Fungal inoculation did not produce considerable changes in gene expression and metabolites in the resistant L4637 inbred, probably due to a preformed or constitutive resistance mechanism. Defense-related genes were induced or repressed in kernels of the susceptible inbred L4674, responding specifically to the pathogen infection. The qRT-PCR in infected silks showed that glucanase, lipid transfer, xylanase inhibitor, PR1 and 26S proteosome transcripts had higher expression ratios in the susceptible line compared to the resistant one in response to fungal infection. Through this study, a global view of differential genes expressed and metabolites concentration during resistance and susceptibility to F. verticillioides inoculation has been obtained, giving additional information about the mechanisms and pathways conferring resistance to this important disease in maize. Global view of differential genes expressed during resistance and susceptibility to F. verticillioides inoculation. Two maize inbred lines : one resistant (L4637) and one susceptible (L4674) to F. verticillioides infection. Two-condition experiment, Inoculated (I) vs. non-inoculated (NI) lines. Biological replicates: 3 . One replicate per array.
2013-08-17 | E-GEOD-40288 | biostudies-arrayexpress
Project description:Fusarium verticillioides is a detrimental fungus that can contaminate maize grains with mycotoxins that are harmful to human and animal health. Breeding and growing resistant genotypes is one alternative to reduce contamination and subsequent production of mycotoxins by this fungus. However, little is known about the resistant mechanism relevant to breeding in this pathosystem. Therefore, our aim was to identify genes and metabolites that may be related to Fusarium ear rot resistance using resistant and susceptible maize inbreds. Kernels of the resistant inbred showed significantly reduced disease severity, and reduced levels of total fumonisin and ergosterol content compared with the susceptible one. Gene expression data were obtained from microarray hybridizations using F. verticillioides inoculated and non inoculated maize kernels. Differentially expressed sequences were identified and classified into 36 functional categories. Most of the differentially expressed genes were assigned to the categories “protein, RNA, DNA, stress, transport, signaling and cell metabolism”. These genes encode for PR proteins, detoxification and primary metabolism enzymes. Fungal inoculation did not produce considerable changes in gene expression and metabolites in the resistant L4637 inbred, probably due to a preformed or constitutive resistance mechanism. Defense-related genes were induced or repressed in kernels of the susceptible inbred L4674, responding specifically to the pathogen infection. The qRT-PCR in infected silks showed that glucanase, lipid transfer, xylanase inhibitor, PR1 and 26S proteosome transcripts had higher expression ratios in the susceptible line compared to the resistant one in response to fungal infection. Through this study, a global view of differential genes expressed and metabolites concentration during resistance and susceptibility to F. verticillioides inoculation has been obtained, giving additional information about the mechanisms and pathways conferring resistance to this important disease in maize.
2013-08-17 | GSE40288 | GEO
Project description:An gene-expression comparison of the wild type and strain delta-fst1 of Fusarium verticillioides grown on autoclaved maize kernels for six days was conducted.
2015-02-19 | GSE66044 | GEO
Project description:F. verticillioides cultured on dissected maize tissues. Keywords: Differential gene expression
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Project description:Fusarium verticillioides (F. verticillioides) stalk rot is one of the most devastating diseases of maize that causes significant yield losses and poses potential security concerns of foods worldwide. The underlying mechanisms of maize plants regulating defense against the disease remain poorly understood. Here, integrative proteomic and transcriptomic analyses were employed to identify pathogenies-related protein genes by comparing differentially expressed genes (DEGs) and proteins (DEPs) in maize stalks after inoculated with F. verticillioides.
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Project description:The present study profiled and analyzed gene expression of the maize ear at four key developmental stages. Based on genome-wide profile analysis, we detected differential mRNA of maize genes. Some of the differentially expressed genes (DEGs) were predicted to be potential candidates of maize ear development. Several well-known genes were found with reported mutants analyses, such as, compact plant2 (ct2), zea AGAMOUS homolog1 (zag1), bearded ear (bde), and silky1 (si1). MicroRNAs such as microRNA156 were predicted to target genes involved in maize ear development. Antisense transcripts were widespread throughout all the four stages, and are suspected to play important roles in maize ear development. Thus, identification and characterization of important genes and regulators at all the four developmental stages will contribute to an improved understanding of the molecular mechanisms responsible for maize ear development. Seeds of the maize inbred line 18-599 (Maize Research Institute, Sichuan Agricultural University, Chengdu, China) were grown in a growth chamber at 24°C/18°C (day/night) with 12 h illumination per day. Ears were collected as described previously [10] at four developmental stages: the growth point elongation, spikelet differentiation, floret primordium differentiation, and the floret organ differentiation phases. In brief, ears were manually collected at the four developmental stages. All the samples were harvested and immediately frozen in liquid nitrogen, and stored at -80°C until used for RNA isolation.
2015-04-30 | E-GEOD-49805 | biostudies-arrayexpress
Project description:Genome-wide expression signatures detect specific perturbations in developmental programs and contribute to functional resolution of key regulatory networks. In maize (Zea mays) inflorescences, mutations in the RAMOSA (RA) genes affect determinacy of axillary meristems and thus alter branching patterns, an important agronomic trait. In this work, we developed and tested a framework for analysis of tag-based, digital gene expression (DGE) profiles using Illumina’s high-throughput sequencing technology and the newly-assembled B73 maize reference genome. We also used a mutation in the RA3 gene to identify putative expression signatures specific to stem cell fate in determinacy of axillary meristems. The RA3 gene encodes a trehalose-6-phosphate-phosphatase and may act at the interface between developmental and metabolic processes. Deep sequencing of DGE libraries, representing three biological replicate ear samples from wild-type and ra3 plants, generated 27 million 20-21nt reads with frequencies spanning four orders of magnitude. Unique sequence tags were anchored to 3´-ends of individual transcripts by DpnII and NlaIII digests, which were multiplexed during sequencing. We mapped 86% of non-redundant signature tags to the maize genome, which associated with 37,117 working gene models and un-annotated regions of expression. 66% of maize genes were detected at ≥ nine reads in immature maize ears. We used comparative genomics to leverage existing information from Arabidopsis and rice in functional analyses of differentially expressed maize genes. Results from this study provide a basis for analysis of short-read expression data in maize and resolved specific expression signatures that will help define mechanisms of action for the RA3 gene.
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Project description:Trichoderma species can stimulate local and distant immune responses in colonized plant tissues to prevent future pathogenic attacks. Priming of plant defenses is characterized by changes on transcriptional, metabolic, and epigenetic states after stimulus perception. We have previously investigated the transcriptional reprogramming in silk tissues from maize plants inoculated with Trichoderma atroviride and challenged with Fusarium verticillioides (Agostini et al 2019). To better understand about the molecular changes induced by T. atroviride in maize, a proteomic approach was conducted in this instance. Several proteins belonging to different metabolic categories were detected as priming involved proteins. However, we detected a very low correlation with those priming-modulated transcripts suggesting the importance of regulatory events posteriori of transcriptional stage to accomplish the final goal of blocking the pathogen entrance. Specifically, we focused on phenylpropanoid pathway; since we detected several proteins that are upregulated in priming state might explain the cell wall reinforcement and, the increase in the content of flavonoids and lignin in silks of maize plants after induced systemic resistance activation.
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Project description:A next-generation RNA-sequencing approach was used for the first time to study transcriptional changes associated with Fusarium verticillioides inoculation in resistant CO441 and susceptible CO354 maize genotypes at 72 hours post inoculation.
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