Elucidation of Gene Regulatory Networks Involved in Nodule Development in Soybean

Biological nitrogen fixation in root nodules of soybean and other agricultural legumes helps reduce reliance on chemical fertilizers providing both economic and environmental benefits. Root nodule development involves large scale gene regulation. Our study presents a robust computational framework to predict gene regulatory networks (GRN) involved in root nodule development. A genome-scale expression dataset was obtained from soybean root nodules and lateral roots and subjected to biclustering using QUBIC. Biclustered dataset and transcription factor (TFs) genes with specific expression in root nodule tissues were converged in two different network inference algorithms to infer confident regulatory modules associated with nodule development. The combination of results from different network inference algorithms into one ensemble solution identified seven GRN modules of co-regulated genes potentially involved in nodule development in soybean. Besides, tissue wise expression, comparison with public data, enrichment of GO, and cis-regulatory motif analyses indicated that a homoedomain like protein, homeobox protein and integrase-type DNA binding TFs, co-regulate GRN modules during early nodule development; and TFs such as AP2, LOB and GRAS co-regulated GRN modules late during nodule development. Knowledge from this work supported by experimental validation in the future is expected to help determine key gene targets for biotechnological strategies to optimize nodule formation and enhance nitrogen fixation.