Genome-Wide Identification, Characterization, Expression Analysis, and Interacting Protein Prediction of the GSK3/Shaggy-like Gene Family in Watermelon

Glycogen synthase kinase 3 (GSK3/Shaggy-like) is a highly conserved serine/threonine kinase that orchestrates growth, hormone signaling, and abiotic stress responses in both animals and plants, yet its role in watermelon remains unexplored. In this study, we conducted a whole-genome identification, identifying a total of eight members of the GSK3 gene family (ClGSK3) distributed across seven chromosomes. Phylogenetic and synteny analyses resolved the eight ClGSK3s into four subfamilies that display one-to-one or one-to-many orthology with Arabidopsis and rice GSK3 genes, indicating conserved genomic micro-collinearity across dicots and monocots. Predictions of cis-acting elements and transcriptome data analysis indicate that ClGSK3s may be involved in hormone- and stress-responsive conditions. Protein–protein interaction networks predicted 53 candidate partners for five ClGSK3 proteins; yeast two-hybrid assays subsequently confirmed that ClSK21 associates with three of them—orthologs of the core brassinosteroid (BR)-signaling components BKI1 and BZR1. qRT-PCR revealed that ClSK21, ClSK31, and ClSK41 are rapidly and significantly reprogrammed by BR treatment. Collectively, our data suggest that ClGSK3s modulate fruit development and stress tolerance by integrating hormone-related pathways, especially BR signaling. Future studies are encouraged to integrate genetics and multi-omics approaches to systematically validate the roles of ClGSK3s in hormone signaling and abiotic stress responses.