Transcriptomic and Metabolomic Investigation of Cell Wall Remodeling and Hormonal Signaling Dysfunction in Short Silique Mutant Rapeseed.

Silique development is a critical factor influencing the yield of rapeseed (B. napus). This study employed the CRISPR/Cas9-mediated BnMYB46 knockout mutant K46 to investigate the molecular mechanisms underlying its short-silique phenotype via integrated cytological, transcriptomic, untargeted metabolomic, and targeted hormone metabolomic analyses. The K46 mutant exhibited significantly reduced silique length, seed number per silique, and dry weight. Cytological observations revealed profound folding of epidermal cells and severe compression of parenchyma cells, consistent with impaired cell expansion. Multi-omics analysis identified plant hormone signal transduction as a core hub pathway disrupted at 20 DAF, and targeted metabolomics confirmed significant endogenous IAA and GA imbalances. qRT-PCR validation showed key hormone genes were significantly altered in K46, with decreases of 22.3-fold in IAA2 and 18.8-fold in GA3OX1 at 20 DAF, and a 165-fold increase in ABF4. These early hormonal disruptions drove downstream suppression of cell wall synthesis and carbohydrate metabolism pathways, leading to impaired cell expansion and compromised structural integrity. This study provides new insights into the hormonal regulatory network governing silique development and identifies potential targets for the molecular improvement of silique-related traits in rapeseed.