Abstract
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.