Transcriptome dynamics of developing maize leaves and genomewide prediction ofciselements and their cognate transcription factors

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. maize transcriptomes | coexpressed genes | cis binding site M aize (Zea mays) is a major crop and a model plant for studying C4 photosynthesis and leaf development. However, the regulatory network that controls maize leaf development is still not well understood. In fact, the number of known maize transcription factor (TF)-binding sites (TFBSs) is far smaller than that for Arabidopsis thaliana (1-3).To understand better the regulation of maize leaf development, several recent studies used next-generation sequencing (NGS) technologies to survey transcriptomic differences among maize leaf cell types and developmental stages. The first large-scale study was by Li et al. (7) investigated the transcriptomes of Kranz (i.e., the foliar leaf blade) and non-Kranz (the husk leaf sheath) maize leaves to identify cohorts of genes associated with procambium initiation and vascular patterning. Recently, 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.In the present study, we obtained nine transcriptomes of the second leaf from 84-192 h post imbibition at 12-h (6:00 AM and 6:00 PM) or 24-h (6:00 PM only) intervals. Together with the 13 SignificanceMaize is a major crop and a model plant for studying C4 leaf development. However, its regulatory network of leaf ...

A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants

“…A widely used approach to elucidate the function of a TF is to perturb the given TF and compare expression profiles of the wild-type and perturbed states, leading to lists of differentially expressed genes on which de novo motif finding often is performed to obtain new insights on the regulation of these genes. The combination of these motifs with conservation analysis is a powerful approach to identify genome-wide bona fide target genes with these motifs and can help to unravel the underlying regulatory cascade, as was shown recently for leaf development in maize (Zea mays; Yu et al, 2015). Another approach in which CNSs can play a key role is the translation of existing knowledge of GRNs in model species into economically more interesting species, which is not trivial, owing to the occurrence of evolutionary changes.…”

Combined Large-Scale Phenotyping and Transcriptomics in Maize Reveals a Robust Growth Regulatory Network

“…Transcriptomes of different regions of a growing leaf, representing different developmental stages, were compared by Li et al (2010) and Pick et al (2011). Transcriptional dynamics during early development of embryonic leaves were surveyed by Liu et al (2013b) and Yu et al (2015). Additionally, the regulatory and functional differentiation of various leaf cell types was examined by transcriptome analysis (Li et al, 2010;Wang et al, 2013Wang et al, , 2014.…”

“…Although analyses of transcriptional variation during maize leaf development have provided us with new insights, all these studies were restricted to one genetic background (Li et al, 2010;Pick et al, 2011;Liu et al, 2013b;Wang et al, 2013Wang et al, , 2014Yu et al, 2015). Adding an additional layer of information, phenotypic variation in mapping populations, and combining this with transcriptome variation in these populations offers new opportunities to identify genes and regulatory mechanisms that are at the basis of phenotypic differences (Andorf et al, 2012).…”

<i>De novo</i> Short Read Assembly and Functional Annotation of <i>Eleocharis vivipara</i>, a C₃/C₄ Interconvertible Sedge Plant

“…5A and B) revealed that unigenes belonging to 13 MapMan bins might have been enriched during the C4-associated evolution (Supplementary Table S12). Among the enriched unigenes, those assigned to the "Cell wall", "RNA", and "Development" classes, which have been pointed out to contribute to the differentiation and development of C4 -specific mesophyll and bundle-sheath cells (Chang et al, 2013;Yu et al, 2015), were found. For example, 4 of the SCARECROW genes and 2 of SHORT ROOT genes both of which are suggested to be involved in the development of bundle sheath cells Gao et al, 2014) and 2 of the nodulin (Nodule inception 1 genes which are reported to be involved in vascular strand formation in gramineous plants (Gamas et al, 1996) and Kranz structure development (Chang et al, 2012) were found in the "Development" class.…”