miR160 Action and Transcriptome Profiles Suggest that Root Nodules might have Evolved from Shoot Lateral Organs

We used global gene and microRNA (miRNA) expression profiles to identify potential candidates that might play key roles in soybean nodule development. Comparative expression analysis of miRNAs and their potential target genes identified key miRNA-target pairs potentially involved in nodule development. Of particular interest to us was miR160 that regulates the levels of repressor auxin response transcription factors belonging to the ARF10/16/17 family. We observed an inverse expression pattern between miR160 and the majority of its validated targets. We evaluated the functional significance of miR160 levels through ectopic expression and suppression assays combined with hormone response assays, fluorescent sensor microscopy, and hormone rescue assays. Results from these experiments indicated that miR160 dictates developmental stage-specific balance between auxin and cytokinin to direct proper nodule formation and maturation in soybean. Interestingly, both miR160 activity and auxin-cytokinin balance required during nodule formation is similar to that of shoot axillary meristems and opposite to that of lateral root meristems. In addition, members of genes families associated with shoot axillary meristem formation were enriched in nodules, but not lateral roots in our transcriptome datasets. These observations provide strong support to the hypothesis that nodule formation might have evolved by recruiting developmental and hormonal signaling pathways from shoot axillary bud formation.