This renewal proposal uses a combination of plant breeding, molecular biology, bioinformatics, and genomic methodologies to discover new genes in order to improve soybean nodulation under a wide range of normal and stress conditions, Identifying genes that can be used to enhance nodulation efficiency and nitrogen fixation will certainly enhance amino acid biosynthesis and protein content in soybean seeds. During the last two years of this TSPB funding project we generated various libraries and completed the bioinformatics analysis of gene expression patterns, and epigenetic profiles of three nodule developmental states (initiation, formation, and senescence) for the first time in soybean. Also, we identified the complete set of differentially spliced genes (genes that produce different proteins) using a comprehensive platform of genomic and bioinformatics tools. These unique dataset place our team in excellent position to carry-out a functional characterization of gene candidates to prove their functions in enhancing nodule number, size, life span, nitrogen fixation and most importantly seed yield and quality as a logic next step of this project.