Genome-Wide Identification and Expression Analysis of the GDPD Gene Family in Cucumber (Cucumis sativus L.)

Glycerophosphate diester phosphodiesterase (GDPD) catalyzes the decomposition of glycerophosphate diester into sn-glycerol-3-phosphate and corresponding alcohols. In this study, six GDPD genes were identified in the cucumber genome, named CsGDPD1 to CsGDPD6, and distributed on chromosomes 1, 3, 4, 5, 6, and 7. All six proteins exhibited similar predicted three dimensional structures, suggesting conserved biochemical functions. Phylogenetic and dN/dS selection pressure analyses revealed that CsGDPD genes are evolutionarily close to their Arabidopsis homologs and have evolved under purifying selection, indicating functional conservation. Synteny analysis identified five collinear gene pairs between cucumber and Arabidopsis, but no synteny with rice. Promoter cis-acting element analysis showed the presence of multiple stress- and hormone-responsive elements. Tissue-specific expression profiling demonstrated that CsGDPD1, CsGDPD2, and CsGDPD6 are broadly expressed across tissues, whereas CsGDPD4 and CsGDPD5 show preferential expression in reproductive organs. qRT-PCR under drought and salt stress, with or without the plant growth promoting rhizobacterium GD17, revealed that drought alone upregulates all CsGDPD genes; PGPR-GD17 alone (+PGPR) suppresses their expression; and combined PGPR + Drought leads to synergistic suppression. Under salt stress, CsGDPD5 was dramatically upregulated (20-fold), and PGPR-GD17 partially reversed salt induced changes. These results provide a comprehensive foundation for understanding the evolutionary and functional roles of the GDPD gene family in cucumber stress responses.