COCHLEATA controls spatial regulation of cytokinin and auxin during nodule development

Root nodules host nitrogen-fixing bacteria and likely evolved through modifications of the lateral root program. Members of the NOOT-BOP-COCH-LIKE transcriptional coregulator family suppress root identity in nodules and plant hormones play key roles in nodule organogenesis, but the interaction between these pathways is unclear. In this study, we investigate how COCH regulates nodule identity through crosstalk with plant hormones, using the Pisum sativum cochleata (Pscoch) mutant - which forms root-nodule hybrids - in combination with hormone biosensors, double mutants, hormone quantification, and RNA-seq analysis. We found that COCH suppresses cytokinin levels and response during nodule formation. By contrast, PsCOCH promotes auxin accumulation and precise auxin response patterning in nodules. Mutant coch developing nodules have gene expression profiles more similar to that of root primordia, with increased expression of defence and auxin response genes and reduced expression of cytokinin biosynthesis genes compared to wild-type. We found gibberellin is unlikely to act downstream of PsCOCH. Constitutive expression of PsCOCH also produces root-nodule hybrids and we found intriguing links between the autoregulation of nodulation pathway and PsCOCH. We show that PsCOCH is required for spatial tight regulation of auxin and cytokinin during nodule organogenesis and identify key hormone and signalling genes that act downstream of COCH.