Light-sensitive short hypocotyl genes confer symbiotic nodule identity in the legume Medicago truncatula

Legumes grow specialized root nodules that are distinct from lateral roots in morphology and function, with nodules intracellularly hosting beneficial nitrogen-fixing bacteria that provide the plant with nitrogen. We have previously shown that a lateral root-like program underpins nodule initiation, but there must be additional developmental programs that confer nodule identity. Here, we show that two members of the LIGHT SENSITIVE SHORT HYPOCOTYL (LSH) transcription factor family, known to define organ boundaries and meristem complexity in the shoot, function as regulators of nodule organ identity. LSH1/LSH2 function upstream of and together with the known nodule regulators Nuclear Factor Y A1 and NODULE ROOT1/2. The principal outcome of LSH1/LSH2 function is the production of cells able to accommodate nitrogen-fixing bacteria, a unique nodule feature. We conclude that the coordinate recruitment of a pre-existing shoot developmental program, in parallel to a root program, underpins the divergence between lateral roots and nodules. RNAseq of M. truncatula genes after rhizobia (S. meliloti 2011) treatment in wild type (R108), and mutants: lsh1-1, lsh1lsh2, noot1noot2, nf-ya1-1, RNAseq of M. truncatula genes with the ectopic expression of LSH1LSH2 and NOOT1NOOT2