Maize plants (Zea may) : WT (Alice) vs. Yellow stripe mutants (ys1 or ys3) (qPCR)
Ontology highlight
ABSTRACT: qPCR gene expression profiling of Yellow stripe 1 (ys1) and ys3 mutants. ys1 and ys3 are recessive mutants of maize (Zea mays L.) that result in symptoms typical of Fe deficiency, i.e., interveinal chlorosis of the leaves. The objective of the present work was to identify the genes involved in the ys1 and ys3 phenotypes, so as to extend our understanding of Fe homeostasis in maize. Root or shoot of WT vs. ys1 or ys3 mutants under Fe sufficient or Fe deficient conditions respectively.
Project description:Transcriptional profiling of Yellow stripe 1 (ys1) and ys3 mutants. ys1 and ys3 are recessive mutants of maize (Zea mays L.) that result in symptoms typical of Fe deficiency, i.e., interveinal chlorosis of the leaves. The objective of the present work was to identify the genes involved in the ys1 and ys3 phenotypes, so as to extend our understanding of Fe homeostasis in maize. Root or shoot of WT vs. ys1 or ys3 mutants under Fe sufficient or Fe deficient conditions respectively.
Project description:Transcription profiling of citrus rootstock Poncirus trifoliata (L.) Raf. Keywords: Abiotic stress (Iron chlorosis) Total RNA from four replicates for each sample category (Poncirus trifoliata (L.) Raf watered for 60 days with 18 uM Fe-EDDHA or without Fe-EDDHA) were generated and compared.
Project description:Purpose: Zinc deficiency (ZnD) and iron deficiency (FeD), excess Zn (ZnE) and cadmium exposure (CdE) are major environmental problems for crop cultivation. Methods: Applying Tag-Seq technology to leaves of Brassica rapa grown under FeD, ZnD, ZnE or CdE conditions, with normal conditions as a control, we examined global gene expression changes and compared the expression patterns of multiple paralogs. Results: We identified 812, 543, 331 and 447 differentially expressed genes under FeD, ZnD, ZnE and CdE conditions, respectively, in B. rapa leaves.Further analysis revealed that genes associated with Zn, Fe and Cd responses tended to be over-retained in the B. rapa genome. Most of these multiple-copy genes showed the same direction of expression change under stress conditions. Conclusion: We conclude that the duplicated genes involved in trace element responses in B. rapa are functionally redundant, making the regulatory network more complex in B. rapa than in Arabidopsis thaliana. In total, there were 15 Digital gene expression libraries, one for each of the three replicates under the four trace metal element treatments and normal nutrient supply conditions as a control.
Project description:Transcriptional profiling of rice genes analyzing the effect of knockdown of OsHRZ1 and OsHRZ2 in HRZ2i lines. NT and HRZ2i lines 1, 2 and 3 (2i-1, 2i-2 and 2i-3, respectively) were treated under iron sufficiency for 7 days (+Fe 7d) or under iron deficiency for 1 day (-Fe 1d) or 7 days (-Fe 7d) in hydroponic culture. Comparison between NT and HRZ2i lines at +Fe 7d, -Fe 1d and -Fe 7d. Biological replicates: 2-3 NT replicates, 3 HRZ2i replicates (one each for 2i-1, 2i-2 and 2i-3) for each treatment.
Project description:Low phosphate concentrations are frequently a constraint for maize growth and development, and therefore, enormous quantities of phosphate fertilizer are expended in maize cultivation, which increases the cost of planting. Low phosphate stress not only increases root biomass but can also cause significant changes in root morphology. Low phosphate availability has been found to favor lateral root growth over primary root growth by dramatically reducing primary root length and increasing lateral root elongation and lateral root density in Arabdopsis. While in our assay when inbred line Q319 subjected to phosphate starvation, The numbers of lateral roots and lateral root primordia were decreased after 6 days of culture in a low phosphate solution (LP) compared to plants grown under normal conditions (sufficient phosphate, SP), and these differences were increased associated with the stress caused by phosphate starvation. However, the growth of primary roots appeared not to be sensitive to low phosphate levels. This is very different to Arabidopsis. To elucidate how low phosphate levels regulate root modifications, especially lateral root development, a transcriptomic analysis of the 1.0-1.5 cm lateral root primordium zone (LRZ) of maize Q319 treated after 2 and 8 days by low phosphate was completed respectively. The present work utilized an Arizona Maize Oligonucleotide array 46K version slides, which contained 46,000 maize 70-mer oligonucleotides designated by TIGR ID, and the sequence information is available at the website of the Maize Oligonucleotide Array Project as the search item representing the >30,000 identifiable unique maize genes (details at http://www.maizearray.org). Keywords: low phosphate, Lateral Root Primordium Zone, maize Two-condition experiment, low phosphate treated lateral root primordium zone of maize root vs. normal cultrued lateral root primordium zone. Biological replicates: 9 control, 9 treated, independently grown and harvested. One replicate per array.
Project description:Through hierarchical clustering of transcript abundance data across a diverse set of tissues and developmental stages in maize, we have identified a number of coexpression modules which describe the transcriptional circuits of maize development. We examined transcript abundance data at 50 developmental stages/tissues of maize, from embryogenesis to senescence, using a custom Affymetrix Unigene array. The VE stage is germination and emergence Vn leaf stage refers to when the collar of the nth leaf is visible.
Project description:au10-14_fer - response of ein3eil1 mutants to fe deficiency - Response of ein3eil1 mutants to Fe deficiency - Wild type seedlings and ethylene insensitive ein3eil1 seedlings were germinated and grown in the presence of 50 µM Fe or absence of Fe (0 µM) on Hoagland medium agar plates until the age of 6 days. Under these growth conditions symptoms of Fe deficiency develop in the 0 Fe plants. Ethylene is known to promote Fe acquisition responses. Whole seedlings were harvested for transcriptome analysis, in a total of three biological replicates. 12 dye-swap - gene knock out,treated vs untreated comparison
Project description:Many of the genes coding for secreted protein effectors are arranged in gene clusters in the genome of the biotrophic plant pathogen Ustilago maydis. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. The generation and analysis strains carrying sub-deletions identified 9 genes significantly contributing to tumor formation after seedling infection. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets. Many of the genes coding for secreted protein effectors are arranged in gene clusters in the genome of the biotrophic plant pathogen Ustilago maydis. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. The generation and analysis strains carrying sub-deletions identified 9 genes significantly contributing to tumor formation after seedling infection. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets. We used the Affymetrix maize genome array to analyze the transcriptional responses of maize to cluster 19A mutants and individual sub-deletions for the cluster 19A genes tin1, tin3, tin4 and tin5. We found plant responses to the mutants were significantly different although the macroscopic phenotypes of the individual mutants were very similar. U. maydis infected parts of maize seedling leaves were dissected 4 days after inoculation with strain SG200∆19A, SG200∆tin1, SG200∆tin3, SG200∆tin4 and SG200∆tin5, respectively. We previously submitted data of maize leaves that were treated with the progenitor wild type strain SG200 as well as mock-infections under identical experimetal conditions (GEO: GSE10023). These data served as controls for this experiment.
Project description:Reduced prolamin (zein) accumulation and defective ER-body formation occurs in maize opaque endosperm mutants opaque2 (o2), floury2 (fl2), defective endosperm*B30 (DeB30), and mucronate (Mc) whereas other opaque mutants such as opaque1 (o1) and floury1 (fl1) are normal in these regards. This suggests that other factors contribute to kernel texture. We used a LC-MS/MS proteomics approach to compare non-zein proteins of nearly isogenic opaque mutants. In total, 2762 proteins were identified that were enriched for biological processes such as protein transport and folding, amino acid biosynthesis, and proteolysis. Amino acid analysis of top proteins revealed qualitative changes in lysine abundance contributing to the overall lysine increase. Principal component analysis and pathway enrichment suggested that the mutants partition into three groups: Mc, DeB30, fl2 and o2; o1; and fl1. Indicator species analysis revealed mutant-specific proteins, and highlighted ER secretory pathway components that are enriched in selected groups of mutants, albeit with no common proteins across all mutants. Most significantly changed proteins were related to stress or defense and zein partitioning into the soluble fraction for Mc, DeB30, o1 and fl1 specifically. We suggest that ER stress is a universal trigger of opacity regardless of qualitative or quantitative changes in zein accumulation.
Project description:Ustilago maydis is a basidiomycete fungus that causes smut disease in maize. Most prominent symptoms of the disease are plant tumors, which can be induced by U. maydis on all aerial parts of the plant. We identified two linked genes, pit1 and pit2, which are specifically expressed during plant colonization. Deletion mutants for either pit1 or pit2 are unable to induce tumor development and elicit plant defense responses. We used the Affymetrix maize genome array to analyze the transcriptional responses of maize to deletion pit1 and pit2 mutants and found plant responses to both mutants being not significantly distinguishable. U. maydis infected parts of maize seedling leaves were dissected 4 days after inoculation with strain SG200Dpit1 and SG200Dpit2, respectively. We previously submitted data of maize leaves that were treated with the progenitor wild type strain SG200 as well as mock-infections under identical experimetal conditions (GEO: GSE10023, 4d mock and 4d SG200 Samples, equivalent record in Arrayexpress: E-GEOD-10023). These data served as controls for this experiment.