HAR1 receptor kinase links nodule autoregulation with repression of auxin signaling and lateral root development.

Nitrogen-fixing root nodules develop as lateral organs on legume roots and their formation is restricted by autoregulation of nodulation (AON), a systemic mechanism with unclear evolutionary origins. We identify Lotus japonicus NUCLEAR FACTOR Y subunit A4 ( NF-YA4 ) gene as a central target of the leucine-rich repeat receptor kinase HAR1, which controls both AON and root system architecture. Under nonsymbiotic conditions, HAR1 suppresses expression of NF-YA4 and its close paralog NF-YA1 , at least in part through a miR169-dependent mechanism, mirroring the Arabidopsis CLAVATA1/2-miR169- NF-YA module. Loss of HAR1 leads to NF-YA4 overexpression, broad transcriptional reprogramming, and induction of LATERAL ORGAN BOUNDARIES DOMAIN , STYLISH , and YUCCA auxin biosynthesis genes, enhancing auxin signaling and lateral root development. Grafting experiments show that HAR1 constrains NF-YA4 -mediated branching both locally in roots and systemically from shoots. Because NF-YA4 functions partly redundantly with NF-YA1 to mediate nodule emergence, our results suggest a model in which duplication and neofunctionalization of an ancestral NF-YA-dependent pathway controlling lateral root development facilitated its recruitment to the nodulation program. They also raise the possibility that AON could have evolved, at least in part, through the co-option of a LRR-RK/miR169/ NF-YA regulatory module that limited lateral root development.