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Background  Calcineurin B-like proteins (CBLs) are major Ca 2+  sensors that interact with CBL-interacting protein kinases (CIPKs) to regulate growth and development in plants. The CBL-CIPK network is involved in stress response, yet little is understood on how CBL-CIPK function in pepper ( Capsicum annuum  L.), a staple vegetable crop that is threatened by biotic and abiotic stressors.    Results  In the present study, nine  CaCBL  and 26  CaCIPK  genes were identified in pepper and the genes were named based on their chromosomal order. Phylogenetic and structural analysis revealed that  CaCBL  and  CaCIPK  genes clustered in four and five groups, respectively. Quantitative real-time PCR (qRT-PCR) assays showed that  CaCBL  and  CaCIPK  genes were constitutively expressed in different tissues, and their expression patterns were altered when the plant was exposed to  Phytophthora capsici , salt and osmotic stress.  CaCIPK1  expression changed in response to stress, including exposure to  P. capsici , NaCl, mannitol, salicylic acid (SA), methyl jasmonate (MeJA), abscisic acid (ABA), ethylene (ETH), cold and heat stress. Knocking down  CaCIPK1  expression increased the susceptibility of pepper to  P. capsici , reduced root activity, and altered the expression of defense related genes. Transient overexpression of  CaCIPK1  enhanced H 2 O 2  accumulation, cell death, and expression of genes involved in defense.    Conclusions  Nine  CaCBL  and 26  CaCIPK  genes were identified in the pepper genome, and the expression of most  CaCBL  and  CaCIPK  genes were altered when the plant was exposed to stress. In particular, we found that  CaCIPK1  is mediates the pepper plant’s defense against  P. capsici . These results provide the groundwork for further functional characterization of  CaCBL  and  CaCIPK  genes in pepper.

Identification of CBL and CIPK gene families and functional characterization of CaCIPK1 under Phytophthora capsici in pepper (Capsicum annuum L.)