Genome-wide characterization of B-box gene family in eggplant and functional identification of SmBBX22 in modulating anthocyanin synthesis

The B-box (BBX) gene family plays a vital role in plant growth, development, and stress responses. This study aimed to characterize the SmBBX gene family in eggplant (Solanum melongena L.), addressing the lack of systematic bioinformatics and functional studies in this species. A total of 33 SmBBX genes were identified through genome-wide analysis. These genes were phylogenetically grouped into five major clades, with shared domain structures, motifs, and genomic architectures among clade members. The gene duplication analysis revealed segmental duplication as the primary mechanism underlying the expansion of SmBBX proteins in eggplant. Additionally, expression profiling across diverse tissues and abiotic stress conditions, combined with the construction of protein–protein interaction networks and luciferase complementation assay, provided valuable insights into the functional roles of SmBBX genes. SmBBX21-2 and SmBBX22 were identified as the key regulators of anthocyanin biosynthesis, activating the expression of SmCHS and SmDFR promoters. Functional validation via heterologous and homologous overexpression demonstrated that SmBBX22 promoted anthocyanin accumulation by upregulating the expression of structural genes (SmCHS, SmF3H, SmF3′5′H, SmDFR, and SmANS) and transcription factors (SmTT8 and SmHY5) important for anthocyanin biosynthesis. Furthermore, the integration of DNA affinity purification sequencing and RNA-seq data revealed the direct transcriptional targets of SmBBX22, including genes involved in secondary metabolism, hormone signaling, and developmental regulation. This highlighted the role of SmBBX22 in phenylpropanoid and flavonoid biosynthesis. This study lays the foundation for understanding the functional roles of BBX genes in eggplant and provides new directions for future research in plant metabolism and stress adaptation.