A Medicago truncatula Autoregulation of Nodulation Mutant Transcriptome Analysis Reveals Disruption of the SUNN Pathway Causes Constitutive Expression Changes in Some Genes, but Overall Response to Rhizobia Resembles Wild-Type, Including Induction of TML1 and TML2 .

Nodule 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 . In the absence of functional SUNN, the autoregulation feedback loop is disrupted, resulting in hypernodulation. To elucidate early autoregulation mechanisms disrupted in SUNN mutants, we searched for genes with altered expression in the loss-of-function mutant and included the autoregulation mutant for comparison. We identified constitutively altered expression of small groups of genes in roots and in shoots. All genes with verified roles in nodulation that were induced in wild-type roots during the establishment of nodules were also induced in , including autoregulation genes and . Only an isoflavone-7-O-methyltransferase gene was induced in response to rhizobia in wild-type roots but not induced in . In shoot tissues of wild-type, eight rhizobia-responsive genes were identified, including a MYB family transcription factor gene that remained at a baseline level in ; three genes were induced by rhizobia in shoots of but not wild-type. We 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 of in roots, a key factor in inhibiting nodulation in response to autoregulation signals, is also triggered in in the section of roots analyzed, suggests that the mechanism of TML regulation of nodulation in may be more complex than published models.