Genome-wide identification of the CIPK gene family in lettuce and expression analysis under salt and drought stress

CBL-interacting protein kinases (CIPKs) serve as key regulators in plant Ca²⁺ signaling pathways, playing a vital role in responding to abiotic stresses such as salinity and drought. However, systematic studies on the CIPK gene family in lettuce (Lactuca sativa L.) remain scarce. In this study, comprehensive identification, structural analysis, evolutionary analysis, and stress response analysis of the CIPK gene family were conducted based on the lettuce reference genome. A total of 32 LsCIPK genes were identified, which were distributed on nine chromosomes. Phylogenetic analysis demonstrated that 32 LsCIPKs could be divided into five evolutionary branches. All LsCIPK proteins contained a typical protein kinase domain and an NAF domain (CBL-interacting domain). Promoter cis-element analysis indicated that most LsCIPK genes are rich in cis-elements associated with light response, hormone response, and abiotic stress. Collinearity analysis indicates that the expansion of this gene family was primarily driven by segmental duplication, and the Ka/Ks ratios for all eight duplicate gene pairs were less than 1, suggesting that the family as a whole is under purifying selection. Expression analysis revealed significant expression changes in multiple LsCIPK genes. Among them, the expression of LsCIPK7, LsCIPK26, and LsCIPK32 was strongly induced. Further qRT-PCR results confirmed the transcriptome trends. Subcellular localization analysis of LsCIPK32 revealed that this protein is primarily distributed in the nucleus and cell membrane. This study provides candidate genes and theoretical support for deciphering the regulatory mechanisms of the lettuce CBL-CIPK signaling pathway and for breeding salt-tolerant and drought-resistant lettuce varieties.