Zea mays subsp. mays
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1054311 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:Maize is one of the most important crops in the world. With the exponentially increasing population and the need for ever increased food and feed production, an increased yield of maize grain (as well as rice, wheat and other grains) will be critical. Maize grain development is understood from the perspective of morphology, hormone responses, and storage reserve accumulation. This includes various studies on gene expression during embryo development and maturation but a global study of gene expression of the embryo has not been possible until recently. Transcriptome analysis is a powerful new tool that can be used to understand the genetic basis of embryo maturation. We undertook a transcriptomic analysis of normal maturing embryos at 15, 21 and 27 days after pollination (DAP), of one elite maize germplasm line that was utilized in crosses to transgenic plants. More than 19,000 genes were analyzed by this method and the challenge was to select subsets of genes that are vitally important to embryo development and maturation for the initial analysis. We describe the changes in expression for genes relating to primary metabolic pathways, DNA synthesis, late embryogenesis proteins and embryo storage proteins, shown through transcriptome analysis and confirmed levels of transcription for some genes in the transcriptome using qRT-PCR.
2012-11-29 | E-MTAB-4393 | biostudies-arrayexpress
Project description:These RNA-seq samples represent ten different tissue types for the fifth version of the maize reference genome B73, sequenced by the NAM Consortium Group. These samples correspond to project ID PRJEB32225.
2020-01-09 | E-MTAB-8628 | biostudies-arrayexpress
Project description:These data include RNA-seq, circRNA-seq, and small RNA-seq of transcriptome, Ribo-seq of translatome and protein protein binary interactions by recombination-based library vs. library yeast-2-hybrid throughout the lifecycle of the maize inbred line B73.
2022-12-25 | GSE160288 | GEO
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.
2013-03-01 | GSE44743 | 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.
2014-10-10 | E-MTAB-4208 | biostudies-arrayexpress
Project description:RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2.
2014-12-05 | E-MTAB-4191 | biostudies-arrayexpress
Project description:Transcriptional profiling of 4 maize varieties comparing genetic root response under control temperature conditions with genetic root response under low temperature conditions
2016-05-24 | GSE72508 | GEO
Project description:Papain-like cysteine proteases (PLCPs) play important roles in plant defense mechanisms. Previous work identified a set of five apoplastic PLCPs (CP1A, CP1B, CP2, XCP2 and CatB) which are crucial for the orchestration of SA-dependent defense signaling and vice versa in maize (Zea mays). One central question from these findings is which mechanism is triggered by apoplastic PLCPs to induce SA-dependent defenses. By a mass spectrometry approach we discovered a novel peptide (Zip1 = Zea mays immune signaling peptide) to be enriched in apoplastic fluid upon SA treatment. Zip1 induces PR-gene expression when applied to naїve maize leaves. Moreover, it activates apoplastic PLCPs similar as SA does, suggesting Zip1 to play an important role in SA-mediated defense signaling. In vitro studies using recombinant protein showed that CP1A and CP2, but not XCP2 and CatB, release Zip1 from its pro-peptide (PROZIP1) in vitro. Strikingly, metabolite analysis showed direct induction of SA de novo synthesis by Zip1 in maize leaves. In line with this, RNA sequencing revealed that Zip1-mediated changes in maize gene expression largely resemble SA-induced responses. Consequently, Zip1 increases maize susceptibility to the necrotrophic fungal pathogen Botrytis cinerea. In summary, this study identifies the PLCP-released peptide signal Zip1, which triggers SA signaling in maize.
2019-02-15 | PXD006751 | Pride
Project description:Profiling transcription levels across many parental inbreds from the maize nested association mapping population.
2013-01-30 | E-MTAB-4328 | biostudies-arrayexpress