Investigating the role of microRNAs in enabling nodulation

To ensure food security we need crops that not only withstand detrimental effects of plant stresses but also have higher productivity. To deal with low nitrogen levels in soil, leguminous plants form a symbiosis with rhizobia soil bacteria in root nodules, enabling nitrogen fixation from the atmosphere. However, nodulation presents something of an evolutionary paradox because it requires a plant to permit invasion by a microorganism without providing a backdoor to be exploited by a bona fide pathogen. It is thought that legumes are able to specifically recognise rhizobia and selectively supress defence responses to allow colonization.
Micro RNAs (miRNAs) are believed to be important mediators of the transition from defence responses to nodulation in legumes. In order to better understand the differences between legumes and non-legumes that allow the former to nodulate, we will use RNAseq to analyse transcriptome expression of non-legumes, including Arabidopsis thaliana, and legumes, including Medicago truncatula, when responding to rhizobia and when undergoing defence responses. Analysis of this data, in combination with miR site predictions, will enable us to make hypotheses about the roles of miRs in defense vs. nodulation across species. We aim to identify miRs whose regulatory action is specific to and conserved during nodulation.
We then aim to use transgenic plants expression GFP specifically in the epidermis, cortex or pericycle and Fluorescence Activated Cell Sorting (FACS) to isolate these single cell types. We can thus test the miR-regulatory predictions and ask at what level of tissue specificity the symbiosis vs. defense responses occur. This will give us a deep understanding of which genes and cell types (with particular attention on miRNAs) are important for regulating the balance between symbiosis and defence in plants.