Study : Zea mays subsp. mays strain:White Crystal Transcriptome or Gene expression

Identification

Name

Zea mays subsp. mays strain:White Crystal Transcriptome or Gene expression

Identifier

dXJuOkVWQS9zdHVkeS9QUkpOQTI1Mzk3Nw==

Source

Data link

Link to this study on EBI European Nucleotide Archive

Description

Maize is a common model plant for studying C4 leaf development because, as a major crop, its genetics is well studied and its genome has been sequenced. However, the regulatory network that controls leaf development remains poorly understood. To tackle this issue, several leaf transcriptomic studies have been conducted. These studies have identified genes differentially expressed between mesophyll and bundle sheath cells or between different regions of a leaf. They have also provided a global picture of the transcriptional dynamics of genes in developing leaves during seed germination. Moreover, one study has identified cohorts of genes associated with procambium initiation and vascular patterning. In the present and a previous study, we have obtained 22 transcriptomes with a time span from hour 0 (dry seeds) to hour 192 post imbibition. Using these time series data, we studied gene up- and down-regulation and functional transition during leaf development, and we inferred 30 sets of strongly coexpressed genes, which showed different functional enrichments. More significantly, we developed methods to predict TF binding sites (TFBSs) and their cognate TFs. In addition, for a TF-TFBS pair known in one species, we developed a method to predict its orthologous TF-TFBS pair in another species. From these efforts, we predicted 1,459 TFBSs and 250 TF-TFBS pairs in the maize genome. Experimental tests of our predicted TF-TFBS pairs showed that our methods perform well. Thus, our study has greatly expanded the information of maize gene regulation during leaf development.

Data files

Genotype

Accession number	Name	Taxon