Natural variation identifies a Pxy gene controlling root vascular organization and formation of nodules and lateral roots in Lotus japonicus

Forward and reverse genetics using the model legumes and have been instrumental for identifying the essential genes governing legume-rhizobial symbiosis. However, little is known about the effects of intraspecific variation on symbiotic signaling. The accessions Gifu and MG20 show differentiated phenotypic responses to the mutant that produces truncated exopolysaccharides. Using Quantitative Trait Locus sequencing (QTL-seq), we identify the gene as a component of this differential response. encodes a leucine-rich-repeat kinase similar to PXY, which regulates stem vascular development. We show that insertion mutants display defects in root vascular organization, as well as lateral root and nodule formation. Our work links to organogenesis in the root, highlights the genetic overlap between regulation of lateral root and nodule formation, and demonstrates that specific natural variants of differentially affect nodulation signaling.