Zea mays subsp. mays
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ABSTRACT:
PROVIDER: PRJNA706018 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Studies of maize diversity to improve crop efficiency: Minimaize
| PRJNA599961 | ENA
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:Development of crop varieties with high nitrogen use efficiency (NUE) is crucial for minimizing N loss, reducing environmental pollution and decreasing input cost. Maize is one of the most important crops cultivated worldwide and its productivity is closely linked to the amount of fertilizer used. A survey of the transcriptomes of shoot and root tissues of a maize hybrid line and its two parental inbred lines grown under sufficient and limiting N conditions by mRNA-Seq has been conducted to have a better understanding of how different maize genotypes respond to N limitation.
2014-01-09 | E-MTAB-4410 | 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: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:Modification of cis regulatory elements to produce differences in gene expression level, localization, and timing is an important mechanism by which organisms evolve divergent adaptations. To examine gene regulatory change during the domestication of maize from its wild progenitor, teosinte, we assessed allele-specific expression in a collection of maize and teosinte inbreds and their F1 hybrids using three tissues from different developmental stages. Our use of F1 hybrids represents the first study in a domesticated crop and wild progenitor that dissects cis and trans regulatory effects to examine characteristics of genes under various cis and trans regulatory regimes. We find evidence for consistent cis regulatory divergence that differentiates maize from teosinte in approximately 4% of genes. These genes are significantly correlated with genes under selection during domestication and crop improvement, suggesting an important role for cis regulatory elements in maize evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem) followed by assessment of allele-specific gene expression.
2014-11-06 | E-GEOD-61810 | 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: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:We analyzed the nucleotide-binding leucine-rich repeat receptors (NLRs) of 26 recently sequenced diverse founder lines from the maize nested association mapping (NAM) population and compared them to the R gene complement present in a wild relative of maize, Zea luxurians.
2023-02-28 | GSE206952 | GEO
Project description:Plant nutrition takes advantage by the simultaneous presence of more N forms in the rhizosphere. In the last decades the interplay between ammonium and nitrate acquisition systems in roots has been deeply investigated. Although widely used as fertilizers, the occurrence of cross connection between urea and ammonium nutrition has been scarcely studied in plants, especially at molecular level. In a recent paper we provided evidence that maize plants fed with urea and ammonium mix showed a better N-uptake efficiency than plants fed with ammonium or urea alone. To elucidate the molecular mechanism underlying this response, transcriptomic and metabolomic changes occurring in maize plants were investigated. Transcriptomic analyses indicated that several transporters and enzymes involved in N-nutrition were found upregulated by all three N-treatments (AMT1.3, NRT1.1, NRT2.1, GS1, GOGAT, GDH), confirming that urea is a direct source of N for plants. Depending on N-form available in nutrient solution a peculiar response at transcriptomic and metabolomic level was observed, especially after 24 hours of treatment. In comparison to one single N-form, urea and ammonium mix induced a prompt assimilation of N, characterized by an overaccumulation of main amino acids in shoots, and an upregulation of ZmAMT1.1. Moreover even a peculiar modulation of aquaporins, carbonic anydrases, glutamine synthetase, amino aspartate, as well as the glycolysis-TCA cycle was induced in roots by urea and ammonium mix. Depending on N-form available in the external media, even changes in phytohormone’s composition were observed in maize (CKs, ABA, JA); in particular, already after 24 hours of treatment, urea induced the accumulation of trans-zeatin in shoots. Through a multiomics approach, we provide for the first time molecular characterization of maize response to urea and ammonium nutrition. This study paves the way to formulate guidelines for the optimization of N fertilization of crops to improve the N use efficiency in plants and therefore limit N losses in the environment.
2021-11-24 | GSE167027 | GEO