Genome-wide identification of BraBES1 genes reveals conserved BR-module features and differential hormone/stress responsiveness in Brassica rapa var. parachinensis

Flowering Chinese cabbage ( Brassica rapa var. parachinensis ) is an important leafy vegetable crop in southern China. BRI1 EMS SUPPRESSOR 1/BRASSINAZOLE RESISTANT 1 (BES1/BZR1) transcription factors are crucial for brassinosteroid (BR) signaling and in coordinating plant growth with stress responses, but their roles in this crop are not well understood. In this study, ten BraBES1 genes encoding proteins with conserved BES1-type DNA-binding motifs were identified in flowering Chinese cabbage. Phylogenetic analysis classified BES1/BZR1 proteins into six groups, designated A–F. The ten BraBES1 proteins from flowering Chinese cabbage were distributed across five of these groups, namely A, C, D, E, and F, with no member assigned to group B. These genes were located on seven chromosomes and showed strong syntenic relationships with their BES1/BZR1 homologs in Arabidopsis thaliana . In transiently transformed tobacco leaves, BraBES1 proteins from groups A, E, and F localized to both the nucleus and cytoplasm, whereas proteins from groups C and D were predominantly nuclear. Yeast two-hybrid assays revealed that all BraBES1 proteins interact with SHAGGY-LIKE KINASE 21 (BraSK21), which is consistent with a conserved BR-associated regulatory module. BraBES1 family members displayed sequence variation, divergent promoter cis -elements, and distinct expression profiles, indicating regulatory divergence within this gene family. Expression analyses under hormone treatments, including brassinolide, gibberellic acid, indole-3-acetic acid, abscisic acid, and salicylic acid, as well as abiotic stresses, including temperature, drought, high light, and salt treatments, showed significant gene-specific responses. In particular, group A genes showed strong responsiveness to hormones and high temperature in the cultivar ‘Sijiu-19’. These findings provide a useful resource for understanding the BraBES1 family and identify candidate genes for functional analysis of BR-linked development and stress adaptation in flowering Chinese cabbage.