Differences in BR perception contribute to hypocotyl length variation in Brassica rapa

Brassica crops exhibit variations in hypocotyl length under natural conditions, and the underlying genetic mechanism remains to be explored. Here, comparative transcriptome analysis revealed that numerous genes differentially expressed between turnip (MM) and Chinese cabbage (BY) at the hypocotyl elongation stage were associated with brassinosteroid (BR)-related pathways. Exogenous application of 24-epibrassinolide (24-epiBL) showed that turnip was more sensitive to 24-epiBL than Chinese cabbage. BrA08BES1, an ortholog of the BRI1-EMS-SUPPRESSOR 1 (AtBES1)/BRASSINAZOLE-RESISTANT 2 (AtBZR2) gene encodes a key transcription factor in the BR signaling pathway and exhibited the highest expression among BrBZR family members in turnip. Effector-reporter-based transactivation assays confirmed that BrA08BES1 activates the transcription of the potential cell expansion gene EXPANSINS 5 (BrA09EXPA5) in both MM and BY. The expression levels of BrA08BES1 and BrA09EXPA5 in turnip are higher than in Chinese cabbage, which is associated with their hypocotyl length. Furthermore, preliminary results from overexpressing BrA08BES1MM in Arabidopsis demonstrate that this gene plays a partial, promotive role in hypocotyl elongation. The present research reveals fundamental differences in BR signaling between turnip and Chinese cabbage. These findings will facilitate future evolutionary and functional studies of hypocotyl phenotype in B. rapa and improve mechanized production efficiency via molecular breeding.