Ascertaining the Co-Expression Networks of Homeobox Genes in Maize

The Shoot Apical Meristem (SAM), from which all aboveground tissues of plants are derived, is critical to plant morphology and development. SAM initiation and development are characterized by distinct transcriptional variation. In maize, loss-of-function mutant studies have identified several well-known SAM related genes, which show distinct SAM-specific expression patterns and act at the top of a hierarchical network including hundreds of genes. Some of these cloned SAM related genes are homeobox genes encoding a typical DNA-binding domain of 60 amino acids, known as a homeodomain, which characterizes a large family of transcription factors. To date, homeobox gene regulatory networks are not well described. Here, we’ve collected a comprehensive transcriptome dataset of 70 different tissues/stages from maize reference inbred-B73, which includes 12 SAM domains of 2-week seedlings and 6 SAMs of different developmental stages. We constructed a co-expression network of 25,351 genes and identified 1,945 SAM-specific expressed genes. Meanwhile, we uncovered 134 homeobox genes using an exhaustive genome-wide search in maize. Examining the co-expression networks, we observed that 104 homeobox genes are involved in 58 different modules, significantly overrepresented in three distinct modules, of which two show SAM-specific expression pattern containing hundreds of other genes with specific DNA-binding motifs. In addition, 32 homeobox genes exclusively from 3 out of 7 homeobox phylogenetic clades are enriched in SAM-specific expression pattern. Our results provide a comprehensive co-expression regulatory network of homeobox genes with respect to SAM development.