Gene switch shapes pepper branching

Pepper growers often face a practical challenge: the same lateral branches that support fruit production can also increase pruning demands and production costs. A new study uncovers a molecular control point behind this balance, showing how one transcription factor promotes branch growth while an interacting energy-related protein restrains it. By tracing the evolution of the BRASSINAZOLE-RESISTANT 1 (BZR1) gene family across plants and testing candidate genes in pepper and tomato, the research identifies CaBZR1.2 as a positive regulator of lateral branch development and CaSnRK1β2 as an opposing factor. The findings provide candidate genes for breeding pepper varieties with plant architectures better suited to different cultivation systems.

Lateral branches are a key part of plant architecture, influencing canopy structure, fruiting sites, yield potential, planting density, and labor input. In horticultural crops such as pepper, tomato, and cucumber, branches often need to be pruned manually, especially when excessive branching interferes with field management. Branch development begins from axillary meristems (AMs), which form axillary buds and later grow into lateral branches. This process is shaped by hormone pathways, including auxin, cytokinin (CK), strigolactone (SL), and brassinosteroid (BR) signaling, yet the role of BR signaling in pepper branching remains insufficiently understood. Due to these problems, in-depth research is needed on the molecular mechanisms regulating lateral branch development in pepper.

The study was conducted by researchers from the College of Horticulture, Hunan Agricultural University; the Vegetable Variety Creation Center, Yuelushan Laboratory; and the College of Landscape Architecture and Horticulture Science, Southwest Forestry University. Published (DOI: 10.1093/hr/uhag015) on January 20, 2026, in Horticulture Research, the study examined the origin and evolution of the BRASSINAZOLE-RESISTANT 1 (BZR1) gene family in plants, identified BZR1 family members in the pepper pan-genome, and functionally characterized CaBZR1.2 in pepper lateral branch development.

The researchers first identified 566 BZR gene family members from 78 plant species, revealing an evolutionary path from charophytes to land plants and later angiosperm diversification. They then screened 14 Capsicum genomes and identified nine pepper BZR1 genes, named CaBZR1.1 to CaBZR1.9. Among them, CaBZR1.2 showed strong relevance because of its conserved sequence features, tissue expression pattern, and nuclear localization of the CaBZR1.2 protein. Using virus-induced gene silencing (VIGS), the team reduced CaBZR1.2 expression in pepper, which significantly shortened lateral branches and reduced branch number. Conversely, heterologous overexpression (OE) of CaBZR1.2 in tomato increased both branch number and branch length. The study also showed that CaBZR1.2 expression was negatively associated with CaBRC1, a gene linked to branch inhibition. Protein interaction assays, including yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), and luciferase complementation imaging (LCI), further demonstrated that CaBZR1.2 interacts with Sucrose Nonfermenting 1-Related Protein Kinase 1 beta subunit 2 (CaSnRK1β2). Silencing CaSnRK1β2 promoted branch elongation, suggesting that CaBZR1.2 and CaSnRK1β2 act antagonistically in shaping pepper branching.

The authors said the study offers a new view of how hormone signaling and energy-related regulation may converge to shape crop architecture. They said CaBZR1.2 appears to act as a promoter of lateral branch growth, while CaSnRK1β2 works in the opposite direction, forming a regulatory balance that may help determine whether axillary buds remain restrained or grow out. This module gives researchers a clearer entry point for studying how pepper plants allocate growth and build productive canopies.

These findings offer practical value for pepper breeding and cultivation. For large-fruited fresh-market peppers, reducing unnecessary branches may help improve planting density and lower pruning labor. For small-fruited or clustered-pod peppers, promoting lateral branching may increase fruiting sites and yield potential. Beyond pepper, the study expands understanding of how BZR1-related transcription factors evolved and diversified in plants. Future breeding may use CaBZR1.2, CaSnRK1β2, and related BR signaling components as molecular targets for marker-assisted selection, transgenic improvement, or gene editing to develop cultivars with more predictable and production-friendly architecture.

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References

DOI

10.1093/hr/uhag015

Original Source URL

https://doi.org/10.1093/hr/uhag015

Funding information

This research was funded by National Nature Science Foundation of China (U22A20497, 32341047, 32302574), Hunan Provincial Natural Science Foundation (2025JJ40022), and Natural Science Foundation of Changsha (kq2506023).

About Horticulture Research

Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.