Genome wide identification of BBP/BPC transcription factor in tomato and its expression profiling in response to abiotic stress

The BARLEY B-RECOMBINANT/BASIC PENTACYSTEINE (BBR/BPC) protein family is one of the smallest transcription factors that binds with GAGA motifs, and it is reported to be involved in growth and development in plants. Even though, the BPC protein was identified earlier its characterization has only been reported in a few plant species. Moreover, no comprehensive genome-wide analysis in tomato has been reported until now. In this study, we identified six BPC genes in the tomato genome and classified them into four groups based on phylogenetic analysis. All the genes had a GAGA domain along with four additional domains found in rice, tomato, and Arabidopsis. Only one segmental duplication gene pair was identified among the tomato genes. In addition, collinearity analysis revealed three duplication pairs between tomato and Arabidopsis, while no duplications were observed between tomato and rice, or rice and Arabidopsis. Environmental stress and hormone-related cis-elements, miRNA, and phosphorylation sites were also identified. Organ-specific expression studies showed that the genes SlBPC2 and SlBPC6 were upregulated in B5 fruit tissues. Additionally, three genes SlBPC1, SlBPC2 and SlBPC6 were upregulated in response to salt, heat, cold, and ABA treatment. The predicted 3D proteins and GO ontology of BPC genes revealed their putative function and their interaction with ligand-binding sites. Subcellular localization fused with GFP protein to the nucleus and the co-expression of SlBPC genes with various defense-related genes, and transcription factor suggest their role in various biological processes. Our findings provide fundamental information about the gene structure and its function which may be helpful for further detailed studies on tomato fruit development, fruit ripening, and abiotic stress tolerance.