Using Genomics Approaches to Study Formation of Nodule-like Structures in Rice

Legumes can develop a symbiotic association with soil bacteria, rhizobia, that leads to the formation of specialized root structures, nodules, inside which nitrogen fixation can occur. Unfortunately, this symbiosis is species-specific and is restricted only to legumes. Therefore, cereals are heavily dependent on fertilizers for their nitrogen needs. Several studies have shown that plant hormones play important roles during legume-rhizobia symbiosis. For instance, auxins induce the formation of nodule-like structures (NLS) on legume roots in the absence of rhizobia.  Furthermore, these NLS can be colonized by rhizobia and successful nitrogen fixation can occur inside them. Interestingly, auxin also induces similar NLS in cereal roots. While several genetic studies have identified plant genes controlling NLS formation in legumes, unfortunately, no studies have investigated the genes involved in NLS formation in cereals. In this study, we were successful in inducing NLS in rice roots, using auxin, 2,4-D, consistently at a high frequency under controlled sterile conditions. These structures were characterized by a broad base, a diffuse meristem, and increased cell differentiation in the vasculature. Next, we performed a comprehensive RNA-Sequencing experiment to identify the differentially expressed genes during NLS formation in rice. We identified several interesting genes based on their biological and molecular functions and we validated the expression pattern of fourteen genes using RT-PCR. Future efforts will focus on identifying and validating the expression pattern of additional genes and genetically characterizing them. These studies will make important advances towards improving nitrogen fixation in cereals and will benefit agriculture.