In silico Promoter Analysis of Photoperiod-Responsive Genes Identified by DNA Microarray in Rice (Oryza sativa L.)

Abstract

The bioinformatics tools, in silico analysis, were used to analyze the promoter regions of photoperiod-responsive genes in rice obtained from microarray analysis. The results revealed that the common feature of a photoperiod-responsive promoter is the combination of various light-responsive elements, hormone-responsive elements and stress-responsive elements. This indicated that the photoperiod response is controlled by light in coordination with hormones and stresses. The coordinated motifs, integrating hormones and stresses to photoperiod responses were identified. The GARE motif and G-box are the coordinated motifs integrating gibberellins with photoperiod while MBS and G-box are the coordinated motifs integrating ethylene or abscisic acid and stresses with photoperiod. Moreover, the specific organization of cis-regulatory elements was used to identify phytochrome A (phyA)-regulated genes. The data showed that phyA is involved in the expression of flowering-time genes either by the activation of floral inducers or the suppression of floral repressors. In addition, two novel cis-regulatory elements which are specific to day-length were identified. The novel A-rich element is specific to long daylight and is involved in the regulation of phyA and circadian rhythm to inhibit flowering whereas the novel GC element is specific to short daylight and involved in the regulation of gibberellin signaling to promote flowering. In conclusion, photoperiodic flowering in rice is controlled, partially, by phyA in coordination with A-rich and GC elements.