Genome-Wide Analysis of Tomato SlCCD Genes and the Role of SlCCD11 in Enhancing Salt Tolerance

Tomato (Solanum lycopersicum L.) is an important horticultural crop. Carotenoid cyclase dioxygenase (CCD) is an enzyme responsible for cleaving carotenoids, which is involved in regulating plant growth and response to abiotic stresses. However, the role of SlCCDs in tomato stress resistance remains unclear. This study used the tomato variety ‘Micro-Tom’ as the material to investigate the function of SlCCDs in stress responses. Through whole-genome analysis, a total of 12 SlCCDs members (SlCCD1–SlCCD12) were identified. Systematic evolutionary analysis classified them into four branches, and members within the same branch maintained a conserved structure. The promoter analysis revealed that SlCCDs contain multiple hormones and stress response elements. The qRT-PCR analysis revealed that SlCCD11 was the most highly expressed gene in the leaves. In addition, multiple SlCCDs showed significant responses to abscisic acid (ABA), methyl jasmonate (MeJA), light, and sodium chloride (NaCl) treatments. Among them, the expression of SlCCD11 significantly increased under salt stress. By silencing SlCCD11 using virus-induced gene silencing (VIGS) technology, it was found that the chlorophyll content, antioxidant enzyme activity, and ABA-related gene expression in the TRV:SlCCD11 plants under salt stress were all lower than the control samples, while the carotenoid content and ROS accumulation were higher. This indicates that SlCCD11 is a positive regulatory factor for salt stress. In conclusion, this study systematically analyzed the SlCCD gene family and revealed the positive role of SlCCD11 in tomato response to salt stress, providing a candidate gene for genetic improvement of crop stress resistance.