Transcriptome analysis ofMedicago truncatulaAutoregulation of Nodulation mutants reveals that disruption of the SUNN pathway causes constitutive expression changes in a small group of genes, but the overall response to rhizobia resembles wild type, including induction ofTML1andTML2

AbstractNodule number regulation in legumes is controlled by a feedback loop that integrates nutrient and rhizobia symbiont status signals to regulate nodule development. Signals from the roots are perceived by shoot receptors, including a CLV1-like receptor-like kinase known as SUNN in the annual medicMedicago truncatula. In the absence of functional SUNN, the autoregulation feedback loop is disrupted, resulting in hypernodulation. To elucidate early autoregulation mechanisms disrupted inSUNNmutants, we searched for genes with altered expression in the loss-of-functionsunn-4mutant and included therdn1-2autoregulation mutant for comparison. We identified constitutively altered expression of small groups of genes insunn-4roots, including higher levels of transcription factorNF-YA2, and insunn-4shoots. All genes with verified roles in nodulation that were induced in wild type roots during the establishment of nodules were also induced insunn-4, including, surprisingly, autoregulation genesTML2andTML1. Among all genes with a differential response to rhizobia in wild type roots, only an isoflavone-7-O-methyltransferase gene (Medtr7g014510) was found to be unresponsive insunn-4. In shoot tissues of wild type, eight rhizobia-responsive genes were identified, including a MYB family transcription factor gene (Medtr3111880) which remained at a baseline level insunn-4; three genes were found to be induced by rhizobia in shoots ofsunn-4but not wild type. We also cataloged the temporal induction profiles of many small secreted peptide (MtSSP) genes in nodulating root tissues, encompassing members of twenty-four peptide families, including the CLE and IRON MAN families. The discovery that expression ofTMLgenes in roots, a key factor in inhibiting nodulation in response to autoregulation signals, is also triggered insunn-4in the section of roots analyzed suggests that the mechanism of TML regulation inM. truncatulamay be more complex than published models.