Microarray based molecular marker detection
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
SUBMITTER: Rowena Kelley
PROVIDER: E-MTAB-766 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Effect of the inactivation of locus PP4959 upon gene expression of P. putida KT2440 in the rhizosphere of corn (Zea mays var. Girona). This locus encodes the unique dual GGDEF/EAL domains response regulator in KT2440. To identify those genes with altered expression, cells were recovered from the rhizosphere six days after inoculation of gnotobiotic seedlings.
2010-06-01 | E-MEXP-2478 | biostudies-arrayexpress
Project description:Maize plants were subjected to foliar herbivory and both whorl and root tissue were collected at 0 h and 24 h. microarray was performed to compare transcriptional profiles and interpret the signaling molecules mediating systemic responses
2011-06-30 | E-MTAB-457 | biostudies-arrayexpress
Project description:Aspergillus flavus is one of the major fungal molds that colonize peanut in the field and during storage. The impact to human and animal health and to economy in agriculture and commerce are significant since this mold produces the most potent natural toxins, aflatoxins, which are carcinogenic, mutagenic, immunosuppressive, and teratogenic. A strain of marine Bacillus megaterium isolated from the Yellow Sea of East China was evaluated for its effect to inhibit aflatoxin formation through down-regulating aflatoxin pathway gene expression in A. flavus as demonstrated by genechip analysis in liquid medium and peanuts. The results showed that aflatoxin accumulation in potato dextrose broth liquid medium and liquid minimal medium was almost totally (more than 98%) inhibited by B. megaterium. The expression of many of the aflatoxin biosynthetic genes in the fungus was confirmed to be turned down. Some of the target genes down-regulated by B. megaterium within the whole genome and within the aflatoxin pathway gene cluster (aflF, aflT, aflS, aflJ, aflL, aflX) were identified. These target genes could be used for controlling aflatoxin contamination in crops such as corn, cotton, and peanut. Importantly, the expression of the regulatory gene aflS was found to be significantly down-regulated. The effect of B. megaterium on aflatoxin biosynthesis and genes expression of pathogen was firstly tested in potato dextrose broth (PDB) and glucose minimal salts medium (MM). The cell suspension of B. megaterium (concentration in PDB and MM was finally adjusted to 108 CFU/ml) or sterile distilled water as a control was added into the 100 ml beaker flask containing 15 ml PDB or MM, respectively. Then 100 M-NM-<l of spore suspension (5 M-CM-^W 106 spores/ml) of A. flavus were added into each beaker flask. After 48 h of incubation at 28M-BM-0C at 200 rpm, mycelia were collected, fresh frozen with liquid nitrogen, ground to a fine powder in liquid nitrogen, and stored at -80M-BM-0C for further analysis. The effect of B. megaterium on aflatoxin biosynthesis and genes expression in the A. flavus fungal pathogen was also tested in two types of peanut kernels, UF 715133-1 and Jinhua 1012, respectively. Peanut kernels were wounded (6 mm diameter and approximately 3 mm deep) using a sterile borer and then 20 M-NM-<l of 1 M-CM-^W 108 CFU/ml cell suspension of B. megaterium was inoculated on wounded peanut kernels respectively. Sterile distilled water was also used for inoculation as control. Two hours after bacterial inoculation, 10 M-NM-<l A. flavus spore suspension was inoculated into each wound at a concentration of 106 spores/ml. The kernels were placed in artificial weather chamber to maintain high humidity (85%) and incubated at 28M-BM-0C for 7 days. Each treatment was replicated three times with 20 peanut kernels in each test. The mycelia on kernels were harvested at day 7 and fresh frozen immediately in liquid nitrogen, ground into powder, and stored at -80M-BM-0C for further analysis.
2013-10-22 | E-GEOD-51469 | biostudies-arrayexpress
Project description:Maize kernels are susceptible to infection by the opportunistic pathogen Aspergillus flavus. Infection results in reduction of grain quality and contamination of kernels with the highly carcinogenic mycotoxin, aflatoxin. To understand host response to infection by the fungus, transcription of approximately 9,000 maize genes were monitored during the host-pathogen interaction with a custom-designed Affymetrix GeneChip® DNA array. More than 1,000 maize genes were found differentially expressed at a fold change of 2 or greater. This included the up regulation of defense-related genes and signaling pathways. Transcriptional changes also were observed in primary metabolism genes. Starch biosynthetic genes were down regulated during infection, while genes encoding maize hydrolytic enzymes, presumably involved in the degradation of host reserves, were up regulated. These data indicate that infection of the maize kernel A. flavus induced metabolic changes in the kernel, including the production of a defense response, as well as a disruption in kernel development. Maize kernels were mock inoculated at the blister (R2) or dough (R4) stage or inoculated with A. flavus at the blister (R2), milk (R3), dough (R4), or dent (R5) stage, and harvested 4 days later. Each treatment consisted of three biological replications. For each biological replication, 8 kernels were ground and RNA was isolated and further processed.
2014-05-14 | E-GEOD-57629 | 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:Herbaspirillum seropedicae is an endophytic bacterium that can fix nitrogen and promote a hormonal imbalance that leads to a plant growth-promoting effect when used as a microbial inoculant. Studies focused on mechanisms of action are crucial for a better understanding of the bacteria-plant interaction and optimization of plant growth-promoting response. The work aims to understand the underlined mechanisms responsible for the early stimulatory growth effects of the H. seropedicae inoculation in maize. To perform it, we combined transcriptomic and proteomic approaches with physiological analysis. The results obtained with the inoculation showed increased root biomass (233 and 253%) and shoot biomass (249 and 264%), respectively, for the fresh and dry mass of maize seedlings and increased green content and development. Omics data analysis for the positive biostimulation phenotype revealed that inoculation increases N-uptake and N-assimilation machinery through differential expressed nitrate transporters and amino acids pathway, as well carbon/nitrogen metabolism integration by the tricarboxylic acid cycle and the polyamines pathway. Additionally, phytohormone levels of root and shoot tissues increased in bacterium-inoculated-maize plants leading to feedback regulation by the ubiquitin-proteasome system. The early biostimulatory effect of H. seropedicae partially results from hormonal imbalance coupled with efficient nutrient uptake-assimilation and a boost in primary anabolic metabolism of carbon-nitrogen integrative pathways.
2023-03-11 | PXD038609 | Pride
Project description:Transcriptional profile of Pseudomonas putida DOT-T1E PS28 grown in the presence of indole (300 uM) compared with the same cells grown in absence of indole.
2013-03-15 | E-MEXP-3825 | biostudies-arrayexpress
Project description:Transcriptional profile of Pseudomonas putida DOT-T1E-18 strain grown in the presence of indole (300 uM) compared with the same cells grown in absence of indole.
2013-03-15 | E-MEXP-3822 | biostudies-arrayexpress
Project description:Transcriptional profile of Pseudomonas putida DOT-T1E grown in the presence of indole (300 uM) compared with the same cells grown in absence of indole.
2013-03-20 | E-MEXP-3819 | biostudies-arrayexpress
Project description:Transcriptional profile of Pseudomonas putida DOT-T1E-18 grown in the presence of ampicillin (100 ug/ml) compared with the same cells grown in absence of ampicillin.
2013-03-15 | E-MEXP-3824 | biostudies-arrayexpress