Genome-Wide Identification of the CBL-CIPK Gene Family in the Ice Plant and Functional Analysis of Salt Stress Tolerance

Background: The ice plant (Mesembryanthemum crystallinum L.) is a typical halophyte with remarkable stress resistance traits, including salinity and alkalinity tolerance. As a crucial signaling transduction pathway for plant responses to environmental stress, the CBL-CIPK signaling system plays a key role in regulating plant stress resistance. Methods: This study systematically analyzed the composition characteristics of the CBL and CIPK gene families across 24 plant species, including the ice plant, using comparative genomics approaches. Results: A total of 297 CBL and 561 CIPK gene family members were identified across the 24 species. Within the ice plant genome, 9 CBL and 18 CIPK genes were identified. Compared to model plants like Arabidopsis thaliana, the ice plant possesses a relatively higher number of CIPK genes, which may be related to its specific adaptation to saline–alkaline environments. Phylogenetic analysis indicated that the ice plant CBL and CIPK genes could be classified into three and four subfamilies, respectively. Expression analysis revealed that several genes (e.g., McCBL1, McCBL4, McCIPK1, McCIPK2) were significantly upregulated under salt stress, suggesting their important roles in the salt stress response. Notably, ice plant CBL and CIPK genes exhibit significant structural diversity. For instance, McCBL3 contains significantly more CDS regions than other members, while CIPK genes can be divided into two types: single-CDS type and multi-CDS type. This structural variation may be associated with functional divergence during the evolution of the gene family. Furthermore, three-dimensional (3D) structure prediction showed that CBL proteins primarily consist of EF-hand domains and α-helices, whereas CIPK proteins additionally contain β-sheet domains, implying that this structural difference may be related to their distinct regulatory mechanisms. Conclusions: This study provides an important theoretical basis for a deeper understanding of the molecular mechanisms underlying the CBL-CIPK signaling pathway in the saline–alkaline stress response of the ice plant.