Genome-Wide Identification of Tomato (Solanum lycopersicum L.) CKX Gene Family and Expression Analysis in the Callus Tissue under Zeatin Treatment

The cytokinin oxidase/dehydrogenase (CKX) enzyme is essential for controlling the fluctuating levels of endogenous cytokinin (CK) and has a significant impact on different aspects of plant growth and development. Nonetheless, there is limited knowledge about CKX genes in tomato (Solanum lycopersicum L.). Here we performed genome-wide identification and analysis of nine SlCKX family members in tomatoes using bioinformatics tools. The results revealed that nine SlCKX genes were unevenly distributed on five chromosomes (Chr.1, Chr.4, Chr.8, Chr.10, and Chr.12). The amino acid length, isoelectric points, and molecular weight of the nine SlCKX proteins ranged from 453 to 553, 5.77 to 8.59, and 51.661 to 62.494 kD, respectively. Subcellular localization analysis indicated that SlCKX2 proteins were located in both the vacuole and cytoplasmic matrix; SlCKX3 and SlCKX5 proteins were located in the vacuole; and SlCKX1, 4, 6, 7, 8, and 9 proteins were located in the cytoplasmic matrix. Furthermore, we observed differences in the gene structures and phylogenetic relationships of SlCKX proteins among different members. SlCKX1-9 were positioned on two out of the three branches of the CKX phylogenetic tree in the multispecies phylogenetic tree construction, revealing their strong conservation within phylogenetic subgroups. Unique patterns of expression of CKX genes were noticed in callus cultures exposed to varying concentrations of exogenous ZT, suggesting their roles in specific developmental and physiological functions in the regeneration system. These results may facilitate subsequent functional analysis of SlCKX genes and provide valuable insights for establishing an efficient regeneration system for tomatoes.