Construction and Application of Functional Gene Modules to Regulatory Pathways in Rice

Signal transduction and transcriptional regulation pathways are key elements in the control of diverse physiological responses and agronomic traits in plants. The regulatory roles of more than 1,000 known genes have been functionally characterized in rice, a model crop plant, and many of them are associated with transcriptional regulation and signal transduction pathways. In this study, we collected and analyzed 417 known genes associated with regulatory pathways, about 40% of the known genes, using the regulation overview installed in the MapMan toolkit. Connecting novel genes to current knowledge about regulatory pathways can elucidate their molecular functions and inspire ideas for further applications. We have summarized the functions of known regulatory genes in the areas of transcriptional regulation, epigenetic regulation, protein modification, protein degradation, signaling and hormone metabolism, also we have emphasized the unique features of several gene families in these classes, including MADS box families, which are strongly associated with the regulation of floral organ identity and flowering time. In addition, our construction of functional modules in four agronomic categories, morphological, physiological, biotic stress and abiotic stress, suggests a basic framework for expanding current knowledge about regulatory pathways to enhance agronomic traits in rice. We also provide a quick illustration of the positive and negative regulatory relationships of the target gene to manipulate agronomic trait by using genome-wide transcriptome data of knockout or overexpression mutations of genes of interest in each functional module.