Genetic and genomic approaches to dissect nodulation in the model legume Medicago truncatula

In response to compatible rhizobia, leguminous plants develop unique plant organs called root nodules, in which rhizobia fix atmospheric nitrogen into ammonia. The aim of this work was to elucidate the plant control of nodulation by identifying and characterizing plant genes that are involved in the symbiotic pathway. This has been achieved by a combined application of functional genomics and molecular genetics in the model legume Medicago truncatula. The first part of this study focused on a novel mutant called lin (for l&barbelow;umpy infections) that initiates symbiotic interactions wherein nodule primordia appear but all infections are arrested in the root epidermis. Genetic mapping has placed this trait on the lower arm of chromosome 1 of M. truncatula with the flanking markers separated by a genetic distance of 3.5 cM. The second phase of this study employed cDNA microarray analysis for functional characterization of lin. In addition to elucidating the molecular phenotype of lin, this analysis also revealed a number of plant genes that could potentially be involved in nodulation. An extensive RT-PCR analysis for homologs of defense and auxin response genes further provided insights in understanding the role of auxin during nodulation and the behavior of defense during early symbiosis. The final part of this study involved a functional analysis of a putative MtCDC16 gene using RNA interference (RNAi) approach. MtCDC16 was selected as a candidate gene from the microarray analysis and a partial suppression of this gene led to a decrease in number of lateral roots and 2-4 times increase in number of nodules. The roots showing lowered expression of MtCDC16 also showed reduced sensitivity to phytohormone auxin. The role of MtCDC16 as one of the molecular mediators in controlling the total number of lateral roots and nodules has been presented in this work.