B-box (BBX) proteins, a subfamily of zinc-finger transcription factors, are involved in various environmental signaling pathways. In this study, we conducted a comprehensive analysis of BBX family members in Brassica crops. The 482 BBX proteins were divided into five groups based on gene structure, conserved domains, and phylogenetic analysis. An analysis of nonsynonymous substitutions and (Ka)/synonymous substitutions (Ks) revealed that most BBX genes have undergone purifying selection during evolution. An analysis of transcriptome data from rapeseed (Brassica napus) organs suggested that BnaBBX3d might be involved in the development of floral tissue-specific RNA-seq expression. We identified numerous light-responsive elements in the promoter regions of BnaBBX genes, which were suggestive of participation in light signaling pathways. Transcriptomic analysis under shade treatment revealed 77 BnaBBX genes with significant changes in expression before and after shading treatment. Of these, BnaBBX22e showed distinct expression patterns in yellow- vs. black-seeded materials in response to shading. UPLC-HESI-MS/MS analysis revealed that shading influences the accumulation of 54 metabolites, with light response BnaBBX22f expression correlating with the accumulation of the flavonoid metabolites M46 and M51. Additionally, BnaBBX22e and BnaBBX22f interact with BnaA10.HY5. These results suggest that BnaBBXs might function in light-induced pigment accumulation. Overall, our findings elucidate the characteristics of BBX proteins in six Brassica species and reveal a possible connection between light and seed coat color, laying the foundation for further exploring the roles of BnaBBX genes in seed development.

Calmodulin-binding transcription activators (CAMTAs) are pivotal regulators decoding calcium signals, with crucial roles in plant development, hormone responses, and adaptation to abiotic stresses. Although extensive research has been conducted on CAMTAs in model plants such as Arabidopsis thaliana, a comprehensive genome-wide analysis of the CAMTA gene family across the economically important Brassica U-triangle species has not been performed. In this study, we systematically identified and characterized 64 CAMTA genes from the genomes of Brassica U-triangle species. Phylogenetic analysis classified these genes into four conserved groups, a finding corroborated by analyses of gene structure and conserved motifs. These analyses revealed strong evolutionary preservation of functional domains, especially the calmodulin-binding domain (CaMBD). Chromosomal distribution and collinearity assessment highlighted the significant impact of polyploidization on the expansion of the CAMTA family, with most orthologous pairs being under purifying selection. Cis-element analysis in promoters uncovered an abundance of stress- and hormone-related elements, suggesting diverse regulatory roles for these genes. Furthermore, RNA-Seq and RT-qPCR expression profiling demonstrated that BnaCAMTA genes exhibit tissue-specific expression and are dynamically responsive to various phytohormones (ABA, JA, and GA) and abiotic stresses (salt and drought), particularly in the root. Notably, BnaCAMTA5.2, which was prioritized among several validated candidates, mediates the antagonistic regulation of hypocotyl and root growth under GA and salt stress, indicating its key role in balancing growth promotion and stress adaptation. Additionally, we identified a set of stress-related miRNAs that potentially target BnaCAMTAs, suggesting a potential layer of post-transcriptional regulation. Our results provide valuable insights into the evolutionary and functional diversity of CAMTA genes in Brassica U-triangle species and lay a foundation for further research into their roles in enhancing stress resistance in B. napus.