In silico analysis of the wheat BBX gene family and identification of candidate genes for seed dormancy and germination

• Published in: BMC plant biology 2024-04, Vol.24 (1), p.334-334, Article 334
• Main Authors: Cheng, Xinran, Lei, Shuying, Li, Jin, Tian, Bingbing, Li, Chunxiu, Cao, Jiajia, Lu, Jie, Ma, Chuanxi, Chang, Cheng, Zhang, Haiping
• Format: Article
• Language: English
• Subjects: Amino acids; Analysis; B-box protein; Bioinformatics; Biosynthesis; Carotenoids; Computer Simulation; Diseases and pests; DNA binding proteins; Dormancy; Gene Expression Regulation, Plant; Gene regulation; Genes; Genes, Plant; Genetic aspects; Genomes; Genomics; Germination; Germination - genetics; Growth; Humidity; Localization; Methods; Multigene Family; Phenotypes; Phylogenetic relationship; Phylogenetics; Phylogeny; Plant Dormancy - genetics; Plant Proteins - genetics; Plant Proteins - metabolism; Pre-harvest sprouting; Proteins; Radiation; Seed dormancy and germination; Seeds; Seeds - genetics; Seeds - growth & development; Transcription; Transcription activation; Triticum - genetics; Triticum - physiology; Two dimensional analysis; Wheat; Zinc finger proteins
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-024-04977-x

B-box (BBX) proteins are a type of zinc finger proteins containing one or two B-box domains. They play important roles in development and diverse stress responses of plants, yet their roles in wheat remain unclear. In this study, 96 BBX genes were identified in the wheat genome and classified into five subfamilies. Subcellular localization prediction results showed that 68 TaBBXs were localized in the nucleus. Protein interaction prediction analysis indicated that interaction was one way that these proteins exerted their functions. Promoter analysis indicated that TaBBXs may play important roles in light signal, hormone, and stress responses. qRT-PCR analysis revealed that 14 TaBBXs were highly expressed in seeds compared with other tissues. These were probably involved in seed dormancy and germination, and their expression patterns were investigated during dormancy acquisition and release in the seeds of wheat varieties Jing 411 and Hongmangchun 21, showing significant differences in seed dormancy and germination phenotypes. Subcellular localization analysis confirmed that the three candidates TaBBX2-2 A, TaBBX4-2 A, and TaBBX11-2D were nuclear proteins. Transcriptional self-activation experiments further demonstrated that TaBBX4-2A was transcriptionally active, but TaBBX2-2A and TaBBX11-2D were not. Protein interaction analysis revealed that TaBBX2-2A, TaBBX4-2A, and TaBBX11-2D had no interaction with each other, while TaBBX2-2A and TaBBX11-2D interacted with each other, indicating that TaBBX4-2A may regulate seed dormancy and germination by transcriptional regulation, and TaBBX2-2A and TaBBX11-2D may regulate seed dormancy and germination by forming a homologous complex. In this study, the wheat BBX gene family was identified and characterized at the genomic level by bioinformatics analysis. These observations provide a theoretical basis for future studies on the functions of BBXs in wheat and other species.