Abstract
Maize is a major crop and a model plant for studying C4 photosynthesis and leaf development. However, a genomewide regulatory network of leaf development is not yet available. This knowledge is useful for developing C3 crops to perform C4 photosynthesis for enhanced yields. Here, using 22 transcriptomes of developing maize leaves from dry seeds to 192 h post imbibition, we studied gene up- and down-regulation and functional transition during leaf development and inferred sets of strongly coexpressed genes. More significantly, we developed a method to predict transcription factor binding sites (TFBSs) and their cognate transcription factors (TFs) using genomic sequence and transcriptomic data. The method requires not only evolutionary conservation of candidate TFBSs and sets of strongly coexpressed genes but also that the genes in a gene set share the same Gene Ontology term so that they are involved in the same biological function. In addition, we developed another method to predict maize TF-TFBS pairs using known TF-TFBS pairs in Arabidopsis or rice. From these efforts, we predicted 1,340 novel TFBSs and 253 new TF-TFBS pairs in the maize genome, far exceeding the 30 TF-TFBS pairs currently known in maize. In most cases studied by both methods, the two methods gave similar predictions. In vitro tests of 12 predicted TF-TFBS interactions showed that our methods perform well. Our study has significantly expanded our knowledge on the regulatory network involved in maize leaf development.
Highlights
Maize is a major crop and a model plant for studying C4 photosynthesis and leaf development
We studied the dynamics of gene expression during the first 192 h of maize embryonic leaf development
Combined with analysis of transcription factors (TFs) expression, our study provides a general picture of transcriptional regulation during this period and highlights the key TF families involved, indicating future directions in elucidating their biological functions in maize leaf development
Summary
Maize is a major crop and a model plant for studying C4 photosynthesis and leaf development. Wang et al [8] conducted comparative transcriptomic and metabolomic analyses of developing leaves in maize and rice and identified putative structural and regulatory components important for C4 and C3 photosynthesis. These studies provided insights into the regulatory mechanisms underlying the development of Kranz leaf anatomy in maize. We developed methods to predict transcription factor-binding sites (TFBSs) and their cognate transcription factors (TFs) or to use the known Arabidopsis TF– TFBS pairs to predict the maize TF–TFBS pairs. Our study has significantly expanded our knowledge of the regulatory network of maize leaf development
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