Zea mays cultivar:B73
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA377727 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5310810.fastq.gz | Fastqsanger.gz | |||
| SRR5310820.fastq.gz | Fastqsanger.gz | |||
| SRR5310811.fastq.gz | Fastqsanger.gz | |||
| SRR5310821.fastq.gz | Fastqsanger.gz | |||
| SRR5310812.fastq.gz | Fastqsanger.gz |
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Project description:Gene transcription is an essential step of gene function and transcriptome variation is of agronomical, ecological and evolutionary importance. To explore global expression patterns and dissect the underlying genetic mechanisms are important scientific inquires which are still largely unknown, especially between a segregating population and the parents. In our study, we used RNA-Seq to profile the shoot apex transcriptome variation (including protein coding genes and non-coding genes) in maize IBM RIL population, to map eQTLs underlying the transcriptome variations and to utilize eQTLs to clone genes involved in maize shoot apices development. We revealed that: Much of the variation (the population mean, the coefficient of variation) of gene expression levels in RILs is reflective of differences present among the parents; These transcriptome variations could be explained by 30,774 eQTLs with 96 trans-eQTL hotspots; In many cases, the genes commonly regulated by a trans-eQTL hotspot are enriched for a specific function or act in the same genetic pathway; Structural variation within and near genes contributs to cis-regulatory variation. All of these results indicate Mendelian factors play as major contributors to the transcriptome variation. Meanwhile, non-Mendelian regulations were also observed as paramutation-like expression pattern for 145 genes, of which 88% genes were predicted to be potential targets of miRNAs or ta-siRNAs, and as unexpected presence/absence expression patterns for 210 genes. These genes with unexpected presence/absence expression patterns in the RILs likely include examples of functional genes as well as transposed gene fragments that may contribute to regulatory variation of their ancestral syntenic genes.
2013-01-30 | E-MTAB-4227 | biostudies-arrayexpress
Project description:We used LM-RNAseq to compare the molecular fingerprints of cells enriched for subdomains within Selaginella, Equisetum, Arabidopsis and maize shoot apices. Three apical domains were isolated from the Selaginella and Equisetum SAMs: the AC domain, comprising the lone AC; the core domain, comprising the cells below the AC and above the initiating leaf primordium; and the initiating leaf primordium. LM-RNAseq analyses of these shoot apical subdomains generated hundreds of significantly DEGs for each cell type relative to whole-plant transcriptomes based on an FDR ⤠0.05. These data were analyzed for the presence of homologous developmental genetic programs across these three species, and for the identification of unique developmental programs operating within each species.
2015-06-17 | E-MTAB-4374 | biostudies-arrayexpress
Project description:chip-seq of Immature ear and Shoot of B73 maize
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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.
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Project description:Phosphoglycerate kinase (PGK, E.C. 2.7.2.3) interconverts ADP + 1,3-bisphospho-glycerate (1,3-bPGA) to ATP + 3-phosphoglycerate (3PGA). While most bacteria have a single pgk gene and mammals possess two copies, plant genomes contain three or more PGK genes. In this study, we identified five Pgk genes in the Zea mays var. B73 genome, predicted to encode proteins targeted to different subcellular compartments: ZmPgk1, ZmPgk2, and ZmPgk4 (chloroplast), ZmPgk3 (cytosol), and ZmPgk5 (nucleus). The expression of ZmPgk3 was highest in non-photosynthetic tissues (roots and cobs), where PGK activity was also greatest, consistent with a function in glycolysis. Green tissues (leaf blade and husk leaf) showed intermediate levels of PGK activity, and predominantly expressed ZmPgk1 and ZmPgk2, suggesting involvement in photosynthetic metabolism. ZmPgk5 was weakly expressed and ZmPgk4 was not detected in any tissue. Phylogenetic analysis showed that the photosynthetic and glycolytic isozymes of plants clustered together, but were distinct from PGKs of animals, fungi, protozoa, and bacteria, indicating that photosynthetic and glycolytic isozymes of plants diversified after the divergence of the plant lineage from other groups. These results show the distinct role of each PGK in maize and provide the basis for future studies into the regulation and function of this key enzyme.
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Project description:As a response to insect attack, maize (Zea mays) has inducible defenses that involve large changes in gene expression and metabolism. Piercing/sucking insects such as corn leaf aphids (Rhopalosiphum maidis) cause direct damage by acquiring phloem nutrients as well as indirect damage through the transmission of plant viruses. To elucidate the metabolic processes and gene expression changes involved in maize responses to aphid attack, leaves of inbred line B73 were infested with R. maidis for two to 96 hours.
2015-09-29 | E-MTAB-5063 | biostudies-arrayexpress
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