Deciphering the Class III Peroxidase Gene Family and Verifying Their Expression in Modulating Seed Germination in Tomato

Seed germination is crucial for seedling establishment and is regulated by precise reactive oxygen species (ROS) signaling. Class III peroxidases (PRXs), which are plant-specific enzymes, play crucial roles in plant growth, development, and responses to abiotic stress by maintaining ROS homeostasis. However, members of the PRX gene family in tomato, particularly their functions in modulating seed germination, remain poorly understood. In this study, 102 tomato PRXs (SlPRXs) were identified, and they were classified into five groups based on phylogenic analysis. Chromosomal localization revealed that these SlPRX genes are unevenly distributed across 12 tomato chromosomes, with chromosome 02 harboring the highest densities. Gene structure analysis revealed that SlPRXs contain 1 to 10 exons, and SlPRX4 possesses the most exons. All SlPRX proteins possess the characteristic peroxidase domain and share conserved structural motifs. Collinearity analysis suggested that segmental duplications might be the main contributor to the expansion of the SlPRX family. Promoter analysis revealed numerous cis-acting elements related to abiotic/biotic stress responses, phytohormones, and growth and development. Notably, seed germination-related elements such as CARE and RY element were identified in some SlPRXs. Enzymatic and electrophoresis assays indicated that PRX activity increased with seed germination. Moreover, SHAM, the inhibitor of PRX, exerted an inhibitory effect on tomato seed germination. Transcriptome data revealed stage-specific induction of SlPRXs during germination, with distinct expression peaks between 0 and 96 h post imbibition. These findings were further validated by qRT-PCR of the selected SlPRX genes. Overall, the findings enhance our understanding of SlPRX family members in tomato and highlight their potential for improving seed germination. This study also provides valuable genetic resources and potential molecular markers for breeding tomato varieties with improved germination vigor and stress resilience.