Genome-Wide Identification of the Tomato PDC Gene Family and Functional Analysis of SlPDC8 in Waterlogging Tolerance

Pyruvate decarboxylase (PDC) is an intracellular non-oxidizing enzyme that relies on thiamine pyrophosphate (TPP), which is important for plant survival under anaerobic conditions and increasingly recognized for its role in broader stress reaction. However, the PDC gene family of tomato (Solanum lycopersicum), an important waterlogging-sensitive agricultural product, has not yet been discovered. In this study, eight SlPDC genes were discovered within the tomato genome. Gene structure analysis revealed that SlPDC members exhibited varying intron–exon configurations, with SlPDC8 possessing the most complex structure containing seven introns. Promoter analysis revealed a multitude of cis-acting elements responsive to light, hormones, and various stresses. Particularly, the promoter of SlPDC8 contains both ABRE and TGACG/CGTCA-motif. Tissue-specific expression profiles showed that SlPDC8 was mainly highly expressed in the roots. Expression profiling demonstrated that SlPDC genes respond divergently to different abiotic stresses, including salt, hydrogen peroxide (H2O2), drought, waterlogging, cold, heat, darkness, and UV radiation stresses. Notably, SlPDC1, SlPDC7, and SlPDC8 were significantly upregulated by waterlogging, with SlPDC8 showing the most robust induction. Functional validation through VIGS proved that SlPDC8-silenced plants exhibited significantly impaired growth, decreased photosynthetic pigment content, severe leaf wilting, and poor root development under waterlogging conditions compared to control plants. Furthermore, silencing SlPDC8 led to increased malondialdehyde (MDA) levels and decreased antioxidant enzyme activities, indicating heightened oxidative damage under waterlogging stress. We conclusively demonstrate that SlPDC8 plays a critical positive regulatory role in waterlogging tolerance by maintaining cellular homeostasis and enhancing antioxidant capacity.