LRM3 positively regulates stem lodging resistance by degradating MYB6 transcriptional repressor in soybean

Summary Stem lodging resistance plays a critical role in maintaining soybean yield stability, yet the molecular mechanisms governing stem development and lodging tolerance remain poorly understood. Here, we report the characterization of lodging‐related mutant 3 ( lrm3 ), a weak‐stemmed soybean line exhibiting increased lodging susceptibility. Molecular cloning revealed that LRM3 encodes a U‐box E3 ubiquitin ligase that physically interacts with the transcription factor MYB6, targeting it for 26S proteasome‐mediated degradation. Transcriptomic and chromatin immunoprecipitation analyses demonstrated that MYB6 binds directly to the promoter regions of PHENYLALANINE AMMONIA‐LYASE ( PAL ) genes, repressing their transcriptional activity and consequently reducing lignin biosynthesis and secondary cell wall deposition in stems. Population genetic analysis identified three major LRM3 haplotypes, with Haplotype 1 preferentially retained in landraces and modern cultivars, suggesting artificial selection during domestication. Collectively, our findings elucidate a previously uncharacterized regulatory mechanism integrating ubiquitin‐mediated proteolysis and phenylpropanoid metabolism to enhance stem mechanical strength. This study provides novel genetic insights and molecular tools for improving lodging resistance in soybean breeding programs.