BrPIF4/BrBBX24-BrHB52-mediated hypocotyl modularity unlocks mechanized harvesting potential in <i>Brassica rapa</i>

Chinese cabbage production faces critical mechanization challenges due to traditional plant architectures that limit mechanical harvesting efficiency. Traditional breeding prioritized short-hypocotyl varieties to prevent damping-off, but long hypocotyls are now critical for mechanical harvesting. We identified BrHB52, an HD-Zip transcription factor, as a key regulator of hypocotyl elongation through quantitative trait locus (QTL) mapping, RNA-seq, and haplotype analysis. <i>BrHB52</i> expression was significantly higher in the long-hypocotyl variety R031L than in the short-hypocotyl variety R032S. Overexpression of <i>BrHB52</i> in both Chinese cabbage and Arabidopsis led to elongated hypocotyls. The silencing of <i>BrHB52</i> in R031L resulted in a reduction of hypocotyl length. Sequence alignment revealed a 251-bp insertion in the <i>BrHB52</i> promoter of the long-hypocotyl variety R031L, which introduced the light-responsive GT-1 motifs. The upstream transcription factors Phytochrome-interacting factor4 (PIF4) and B-box zinc finger 24 (BBX24) were identified through yeast one-hybrid screening using the <i>BrHB52</i> ^<i>R031L</i> promoter sequence. PIF4 were found to bind to the both <i>BrHB52</i> ^<i>R031L</i> and <i>BrHB52</i> ^<i>R032S</i> promoters and activate their expression through G-box, while light-induced factor BBX24 only bind to the <i>BrHB52</i> ^<i>R031L</i> promoter and activate its expression by light-responsive element GT-1. Our findings elucidate a BrPIF4/BrBBX24-BrHB52 regulatory module that controls plant architecture through hypocotyl elongation. These findings not only provide critical genetic targets for developing mechanization-compatible Chinese cabbage, but also develop transgenic prototypes with elongated hypocotyls, offering practical resources for mechanized breeding.