Origin and evolution of <i>BZR</i> gene family in plants, pan-genome analysis of the <i>BZR1</i> gene family and functional characterization of <i>CaBZR1.2</i> in pepper lateral branch development

Abstract The transcription factor BRASSINAZOLE-RESISTANT 1 (BZR1) plays a crucial role not only in plant responses to various biotic and abiotic stresses but also serves a critical function in plant growth and development. In this study, we analyzed the origin and evolution of the BZR family in plants. Then, we identified 9 CaBZR1 genes from the pepper pan-genome and performed bioinformatics analyses. Through the integration of transcriptome data analysis with our prior bioinformatics findings, we have identified and selected a specific member of the CaBZR1 family, CaBZR1.2, for further comprehensive investigation. We systematically investigated the biological function of CaBZR1.2 in pepper through classical reverse genetics approaches and subsequently identified proteins that interact with CaBZR1.2. After inhibiting the expression of CaBZR1.2 via the virus-induced gene silencing (VIGS), the growth of pepper lateral branches was significantly suppressed, whereas heterologous overexpression of CaBZR1.2 increased lateral branch number in tomato. This result confirms the key role of CaBZR1.2 in the development of pepper lateral branches. Furthermore, protein-protein interaction assays confirmed that the Sucrose Non-fermenting 1-Related Protein Kinase 1 β subunit 2 (CaSnRK1β2) protein interacts with CaBZR1.2, with subsequent analyses revealing that these two proteins modulate pepper lateral branch development through a mutually antagonistic regulatory mechanism. This study reveals a novel mechanism by which CaBZR1.2 and CaSnRK1β2 coordinately regulate lateral branch development in pepper, providing candidate genes and a theoretical basis for the molecular breeding of pepper plant architecture.