Spatio-Temporal Gene Expression during Soybean Nodule Development

Soybean, a leguminous plant establishes a symbiotic relationship with nitrogen-fixing rhizobia bacteria resulting in a specialized organ called root nodule. Nodule development initiates from the division of root cortical cells which eventually leads to the formation of the nodule primordium. Further division and differentiation of root cortex cells close to the primordium leads to the formation of nodule parenchyma. In a mature nodule, the parenchyma surrounds the infection zone and houses the nodule vasculature. The infection zone harbors rhizobia bacteria where nitrogen is fixed. The mechanism by which root cortical cells give rise to two structurally and functionally different nodule zones is not known. We seek to fill this knowledge gap by determining the transcriptome profiles of these two nodule zones over a temporal scale, and use the knowledge to identify key signaling determinants in the developmental identity of these zones. We adopted a cell-type specific nuclear tagging method to isolate nuclei from nodule parenchyma (using the ENOD2 promoter) and nodule primordium /infection zone (using the ENOD40 promoter). Using this method, we are able to isolate nuclei with more than 90% purity and more than 50% efficiency. Further isolation of nuclear transcripts, subsequent validation by qPCR, and evaluation of transcriptome profiles by RNAseq will help achieve our goal of identifying key determinants of nodule zone identity. Ultimately, this knowledge is expected to help in optimizing nodulation and nitrogen fixation in leguminous plants. Transfer of this trait to non-leguminous plants for a sustainable solution to our agricultural nitrogen requirements will reducing pollution caused by excessive use of chemical nitrogenous fertilizer and offer cost savings to the farmer.