Transcriptome analysis of Medicago truncatula Autoregulation 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 of TML1 and TML2.

Abstract

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 the annual medic Medicago truncatula. 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 sunn-4 mutant and included the rdn1-2 autoregulation mutant for comparison. We identified constitutively altered expression of small groups of genes in sunn-4 roots, including higher levels of transcription factor NF-YA2, and in sunn-4 shoots. All genes with verified roles in nodulation that were induced in wild type roots during the establishment of nodules were also induced in sunn-4, including, surprisingly, autoregulation genes TML2 and TML1. 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 in sunn-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 in sunn-4; three genes were found to be induced by rhizobia in shoots of sunn-4 but 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 of TML genes in roots, a key factor in inhibiting nodulation in response to autoregulation signals, is also triggered in sunn-4 in the section of roots analyzed suggests that the mechanism of TML regulation in M. truncatula may be more complex than published models.