Genome-Wide Identification of the Potato GGPS Gene Family and Analysis of Its Response to Abiotic Stress

Background: Geranylgeranyl pyrophosphate synthase (GGPS) is a pivotal enzyme in terpene biosynthesis, influencing the production of carotenoids, chlorophylls, and diverse phytohormones. This study aimed to identify and characterize the StGGPS gene family in potato (Solanum tuberosum) to elucidate its involvement in carotenoid synthesis and responses to abiotic stresses. Methods: Employing bioinformatics approaches, including HMMER, SMART, and Pfam, we conducted a genome-wide identification of StGGPS genes. Subsequent phylogenetic analysis, gene structure characterization, conserved motif detection, and synteny analysis were performed to investigate evolutionary relationships within the family. The expression patterns of StGGPS genes were then analyzed using RNA-seq data and quantitative real-time PCR (qRT-PCR) in potato tubers exhibiting different pigmentation and under drought and salt stress conditions. Results: Eleven StGGPS genes were identified, unevenly distributed across seven chromosomes, and classified into three subfamilies based on phylogenetic and structural analyses. Synteny analysis revealed one intra-genomic duplicate pair (StGGPS1/StGGPS4) and conserved orthologs with other Solanaceae species. Promoter analysis identified cis-elements related to light response and abiotic stress (e.g., ABRE and CGTCA-motif). Expression data showed differential regulation of StGGPS genes in colored tubers, with yellow and red tubers exhibiting higher expression of carotenoid-related genes. Under drought stress, StGGPS10 was significantly upregulated (5.2-fold, p < 0.001), while StGGPS6 showed salt-responsive induction (3.8-fold, p < 0.001), linking them to ABA signaling and cytoskeletal dynamics, respectively. Conclusions: This study provides a comprehensive overview of the StGGPS gene family, highlighting their roles in carotenoid biosynthesis and abiotic stress responses. The stress-specific expression patterns of StGGPS10 and StGGPS6 offer potential targets for genetic improvement of potato stress resilience.