Abstract
Maize (Zea mays) is an important crop and feedstock of biofuel. It is also a common model plant for studying the biology of C4 photosynthesis and the development of kranz anatomy, a key structure in C4 plant leaves. Its genome was sequenced in 2009. Through advances in DNA sequencing technologies and bioinformatics skills, genomic and transcriptomic information in maize has become abundant and has facilitated large-scale studies greatly. However, knowledge on the regulatory genomics in the 2GB maize genome is still very limited. Regulatory genomics is the study of the relationship between functional elements and their regulators in a genome. Thus, to study the regulatory genomics of an organism, we need to identify the transcription factors (TFs), transcription coregulators (TCs), transcription factor binding sites (TFBSs) and TF-TFBS relationships. I aimed at gaining a good understanding of the regulatory genomics of maize, from which one can dissect the key regulatory features. I designed bioinformatics methods to study each aspect of the regulatory genomics in maize leaf development. My main focuses are the construction of the modules consisting of TF and TC gene, TFBSs and TF-TFBS pairs. I first annotated 2538 TF genes and 149 TC genes in maize. Because millet (Setaria italica) is another important C4 plant, I also annotated 1880 TF genes and 99 TC genes in millet Yugu1, and 1846 TF genes and 104 TC genes in millet Zhang gu. I provided supporting evidence for my predictions of TF and TC genes from gene expression data in maize or millet and from homologous genes in Arabidopsis or rice. I found that more than 90% of TF and TC genes in maize and millets have homologs in Arabidopsis or rice and more than 75% of maize and millet TF and TC genes were expressed. I evaluated the expression preference of TF and TC genes in tissues in maize and millet and identified 995 TF genes and 71 TC genes in maize and 546 TF genes and 33 TC genes in millet that may potentially contribute to C4 characteristics in the two species. I then collaborated with Dr. Chun-Ping Yu and developed a method that can identify the TFBSs in maize genome by integrating the time-course RNA-seq transcriptome of maize leaf development, maize genome sequence data and available TF-TFBS pairs in other species. We assumed that the TF genes should be coexpressed with their target genes, genes with the same function should possess the same TFBSs and regulated by the same TFs, the functional TFBSs should be conserved in closely related species, and the homologous TFs should still possess similar DNA-binding specificities. We identified 239 maize TF-TFBS pairs for 135 nonredundant maize TFs, achieving a prediction rate of 76%. My study provides the overall work from characterization of TFs and TCs to the TF-TFBS relationship in maize leaf development and the basis for understanding the regulatory network of C4 photosynthesis and Kranz anatomy.