Genome-wide identification of calcium-dependent protein kinase (CDPK) family members in Phaseolus vulgaris L. and expression analysis during abiotic stresses

Background Calcium-dependent protein kinases (CDPKs) are a family of enzymes that are essential in plant signaling pathways. These kinases are activated in response to changes in calcium ion (Ca 2+ ) concentration under stress conditions. Although CDPK gene families have been investigated in various plants, comprehensive genome-wide analyses and expression studies of CDPK genes in Phaseolus vulgaris L. under abiotic stress have not yet been performed. The objective of this research is to perform a genome-wide analysis of the CDPK gene family in common bean and evaluate the expression patterns of these genes under salt and drought stress conditions. Methods This study presents a comprehensive bioinformatics analysis focusing on the phylogenetic relationships, chromosomal distribution, gene structures, conserved motifs, promoter regulatory elements, and expression profiles under salt and drought stress conditions of the CDPK gene family in common bean. Results In this study, 25 PvCDPK genes were identified in the common bean genome. The lengths of proteins vary between 298 and 582 amino acids (aa), and their molecular weights (kDa) range from 33.43 kDa to 65.13 kDa. The majority of the PvCDPKs located on a total of eight chromosomes have six introns. Phylogenetic analysis revealed that PvCDPK proteins are grouped into three major clades along with Arabidopsis thaliana and Glycine max orthologs. The divergence times for six pairs of segmentally duplicated genes ranged from 48.94 million years ago (MYA) to 65.57 MYA, while tandem duplicates ranged from 32.09 to 84.95 MYA. Conclusions Comparative expression analysis of PvCDPK genes revealed varying expression levels depending on the two common bean cultivars. Furthermore, these observations suggest that PvCDPK genes could be essential for the growth and development of common beans in response to abiotic stresses such as drought and salt. This is the first study to investigate the CDPK gene family in common bean, and the identified genes obtained can be directly evaluated as candidate genes for marker-assisted selection or gene editing approaches. In addition, the findings are expected to contribute to the development of resilient cultivars capable of withstanding climate change.