Computational study of environmental stress-related transcription factor binding sites in the promoter regions of maize auxin response factor (ARF) gene family
Auxin response factors (ARF) gene family plays key roles in plant development and act as transcription factors (TFs) in the regulation of gene expression. An extensive bioinformatics analysis including analysis of conserved motifs, chromosomal map, phylogenetic relationships, and expression profiles were performed for the maize ARF gene family. In this study, a set of publicly available 38 ARF maize (Zea mays) nucleotide sequences were downloaded. Using microarray data, a bioinformatics search for identification of TFBs in ARF genes using plant promoter analysis (PlantPAN) was carried out. The 38 maize ARF genes were categorized into three groups (Class I, II, and III). ARF genes have been studied by molecular methods in several different plant species however to better understand the mechanisms of these genes more studies are needed. Gene cluster analysis showed that the same set of genes on the chromosomes were positively correlated with the same number of gene clusters. Several TFBs including AP2/ERF, ERF, WRKY, bZIP, bHLH, GATA, and NAC were identified in the promoter regions. These TFBs are responsible for modulation of several biotic stress-responsive genes. The main aims of the present study were to obtain genomic information for the ZmARF gene family and their expression under abiotic and biotic stresses.