Zea mays
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA747924 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15222100_1.fastq.gz | Fastqsanger.gz | |||
| SRR15222100_2.fastq.gz | Fastqsanger.gz | |||
| SRR15222101_1.fastq.gz | Fastqsanger.gz | |||
| SRR15222101_2.fastq.gz | Fastqsanger.gz | |||
| SRR15222102_1.fastq.gz | Fastqsanger.gz |
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Project description:We demonstrated the manifestation of heterosis in hybrid maize embryo and endosperm tissue six days after fertilization in crosses of several inbred lines. Here we analyzed heterosis-associated gene expression pattern in these tissues of reciprocal crosses of two european maize inbred line combinations. Differences in gene expression were analyzed with custom microarrays by a combined approach of suppression subtractive hybridization and microarray hybridizations
2009-08-28 | GSE17821 | GEO
Project description:Drought represents a major constraint on maize production worldwide. Understanding the genetic basis for natural variation in drought tolerance of maize may facilitate efforts to improve this trait in cultivated germplasm. Here, using a genome-wide association study, we show that a miniature inverted-repeat transposable element (MITE) inserted in the promoter of a NAC gene (ZmNAC111) is significantly associated with natural variation in maize drought tolerance. For maize RNA-seq analysis, pooled tissues from three, eight-day-old maize seedlings were collected from transgenic and wild-type plants, prior to or after 2-hour dehydration, to conduct the RNA-seq analysis.
2015-03-29 | E-MTAB-4246 | biostudies-arrayexpress
Project description:The basidiomycete fungus Ustilago maydis causes smut disease in maize and has become an important model for elucidating the strategies used for host colonization by biotrophic fungi. In this study, we performed an in-depth transcriptional profiling of the plant-associated development of a cross between U. maydis FB1 and FB2 wildtype strains. The analysis of eight different stages, including the development on the leaf surface, early colonization, tumor induction and spore maturation, offers an unprecedented view of the changes in the fungal transcriptome associated with the passage through the entirely biotrophic life cycle. In our analysis, we focus on fungal metabolism, nutritional strategies, secreted effectors and regulatory networks. Secreted proteins were enriched in three distinct expression modules corresponding to the plant surface, establishment of biotrophy and tumor formation, respectively. These modules are likely the key determinants for U. maydis virulence. With respect to nutrient utilization, we observed that expression of several nutrient transporters was tied to these virulence modules rather than being controlled by nutrient availability. We show that oligopeptide transporters likely involved in nitrogen supply during infection are important virulence determinants. By measuring the intramodular connectivity of transcription factors, we identified potential drivers for the virulence modules. While known components of the b-cascade served as inducers for the plant surface and biotrophy module, we identified a set of yet uncharacterized transcription factors as likely responsible for expression of the tumor module. We demonstrate a crucial role in effector gene expression and tumor formation for one of these transcription factors.
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Project description:Signals originating within plastids modulate organelle differentiation by transcriptionally regulating nuclear-encoded genes. These retrograde signals are also integral regulators of plant development, including leaf morphology. The clb5 mutant displays severe leaf morphology defects due to Apocarotenoid Signal 1 (ACS1) accumulation in the developmentally arrested plastid. Transcriptomic analysis of clb5 validates ACS1 as a true retrograde signal impacting expression of hundreds of nuclear genes, including suppression of most genes encoding plastid ribosomal proteins.
2021-06-02 | GSE152252 | GEO
Project description:The prolamin-box binding factor-1 (pbf1) gene encodes a transcription factor that controls the expression of seed storage protein (zein) genes in maize. Prior studies show that pbf1 underwent selection during maize domestication, although how it affected trait change during domestication is unknown. To assay how pbf1 affects phenotypic differences between maize and teosinte, we compared isogenic lines (NILs) that differ for a maize vs.and teosinte alleles of pbf1. Kernel weight for the teosinte NIL (162 mg) is slightly and significantly greater than that for the maize NIL (156 mg). RNAseq data for developing kernels show that the teosinte allele of pbf1 is expressed at about twice the level of the maize allele. However, RNA and protein assays showed no difference in zein profiles between the two NILs. The lower expression for the maize pbf1 allele suggests that selection may have favored this change, however, how reduced pbf1 expression alters phenotype remains unknown. One possibility is that pbf1 regulates genes other than zeins and thereby a domestication trait. The observed drop in seed weight associated with the maize allele of pbf1 is counterintuitive, but could represent a negative pleiotropic effect of selection on some other aspect of kernel composition.
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Project description:Saha2011- Genome-scale metabolic network of
Zea mays (iRS1563)
This model is described in the article:
Zea mays iRS1563: a
comprehensive genome-scale metabolic reconstruction of maize
metabolism.
Saha R, Suthers PF, Maranas
CD.
PLoS ONE 2011; 6(7): e21784
Abstract:
The scope and breadth of genome-scale metabolic
reconstructions have continued to expand over the last decade.
Herein, we introduce a genome-scale model for a plant with
direct applications to food and bioenergy production (i.e.,
maize). Maize annotation is still underway, which introduces
significant challenges in the association of metabolic
functions to genes. The developed model is designed to meet
rigorous standards on gene-protein-reaction (GPR) associations,
elementally and charged balanced reactions and a biomass
reaction abstracting the relative contribution of all biomass
constituents. The metabolic network contains 1,563 genes and
1,825 metabolites involved in 1,985 reactions from primary and
secondary maize metabolism. For approximately 42% of the
reactions direct literature evidence for the participation of
the reaction in maize was found. As many as 445 reactions and
369 metabolites are unique to the maize model compared to the
AraGEM model for A. thaliana. 674 metabolites and 893 reactions
are present in Zea mays iRS1563 that are not accounted for in
maize C4GEM. All reactions are elementally and charged balanced
and localized into six different compartments (i.e., cytoplasm,
mitochondrion, plastid, peroxisome, vacuole and extracellular).
GPR associations are also established based on the functional
annotation information and homology prediction accounting for
monofunctional, multifunctional and multimeric proteins,
isozymes and protein complexes. We describe results from
performing flux balance analysis under different physiological
conditions, (i.e., photosynthesis, photorespiration and
respiration) of a C4 plant and also explore model predictions
against experimental observations for two naturally occurring
mutants (i.e., bm1 and bm3). The developed model corresponds to
the largest and more complete to-date effort at cataloguing
metabolism for a plant species.
This model is hosted on
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and identified by:
MODEL1507180064.
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To the extent possible under law, all copyright and related or
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2015-07-30 | MODEL1507180064 | BioModels
Project description:In this study expression levels of 732 genes were analyzed for European maize (Zea mays L.) inbred lines (4 Flint and 5 Dent) and nine corresponding hybrids by microarray analysis. The selection of the 732 genes was based on a previous study (Thiemann et al., Theor Appl Genet 2010, 120:401-413), which sequences were derived from the 46k microarray (platform GPL6438) (University of Arizona, USA). 558 of the 732 genes represented on the microarray were differentially expressed between the original 21 parental inbred lines and were correlated with at least one of the three characteristics MPH (mid-parent heterosis) and/or HP (hybrid performance) of the trait GY (grain yield) and/or HP of the trait grain dry matter content. Some of those correlated genes show overlapping correlations. The residual 174 non-correlated genes belong to the top 6 biological processes that were found to be enriched among the HP for GY-correlated genes (Thiemann et al., Theor Appl Genet 2010, 120:401–413). The aim of this study was the identification of the hybrid expression pattern of the subset of genes, which mid-parental expression levels were shown to be correlated with MPH for GY or showed no correlation. For the analysis total RNA of 7-day old seedlings was extracted and amino-allyl-labeled RNA was synthesized. The microarrays were scanned (AppliedPrecision ArrayWorx Scanner, Applied Precision Inc., USA) and data were evaluated using the Software GenePix Pro 4.0 (Molecular Devices, Sunnyvale, USA). Hybridizations were conducted between each pair of parental inbred lines and its corresponding hybrids. In total 4 biological replicates per genotype were analyzed. As a result 119 (22.9 %) of the 519 MPH for GY or non-correlated genes showed differential expression in at least one of the nine inbred-hybrid comparisons. These differentially expressed genes were further analyzed for hybrid expression, resulting in a mainly additive expression. Of all differential expression, additive expression of 86.21 % (with 13.79 % non-additive) of the MPH-correlated genes, and a slightly smaller contingent of 79.66 % (with 20.34 % non-additive) of the non-correlated genes was measured.
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Project description:The aim of the present study was to globally survey the transcriptome of the two inbred lines B73 and Mo17 in comparison to their reciprocal F1-progeny in an unbiased approach via RNA-seq using four biological replicates to increase the power for detecting differential expression while maintaining a low false discovery rate (FDR). For this purpose, primary roots of 3.5-d-old seedlings were surveyed, as young primary roots display a very simple structure. This stage was previously demonstrated to precede the first detectable developmental changes between inbred lines and hybrids during heterosis manifestation for numerous root-related traits (Hoecker et al. 2006). By choosing this particular stage, we intended to identify transcriptional patterns and regulators possibly determining the processes leading to heterosis for these early root system traits.
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