COCHLEATA controls spatial regulation of cytokinin and auxin during nodule development

Root nodules develop in some legumes that host nitrogen-fixing bacteria and likely evolved through modifications of the ancestral lateral root program with plant hormones playing key regulatory roles. Members of the NOOT-BOP-COCH-LIKE transcriptional co-regulator family suppress root identity in legume nodules, including Pisum sativum coch that display root-nodule hybrids. However, how COCH/NOOT interacts with hormones to control nodule organogenesis is unclear. We show that PsCOCH (COCHLEATA) is required for spatial tight regulation of auxin and cytokinin during nodule organogenesis and identify key hormone and signalling genes regulated by COCH. COCH suppresses cytokinin levels and response during nodule formation, as cytokinin levels are elevated in Pscoch abnormal nodules and this is mirrored by ectopic cytokinin-responsive TCSn::GUS expression in Pscoch nodule apices, nodule vasculature and in root-like tissue. In contrast, PsCOCH promotes auxin accumulation and precise auxin response patterning in nodules, as Pscoch mutants show significantly reduced auxin levels and severely altered auxin-responsive DR5::GUS expression patterns. RNAseq analysis revealed that Pscoch developing nodules have gene expression profiles more similar to root primordia, with increased expression of defence and auxin response genes (IAA and ARF) and reduced expression of cytokinin biosynthesis genes (IPT3, CYP735A and LOG2) compared to wild type. We found gibberellin is unlikely to act downstream of PsCOCH, as Pscoch and gibberellin-deficient double mutants still form root-nodule hybrids. Ectopic constitutive expression of PsCOCH also produces root-nodule hybrids and we found intriguing links between autoregulation of nodulation pathway and COCH, suggesting that a complex feedback mechanism acts in COCH control of nodule identity.