Genome-wide identification and alkaline stress response analysis of the class III peroxidase (PRX) gene family in Castanea mollissima

Class III peroxidases (PRXs) are plant-specific proteins crucial for growth, development, and stress responses. Castanea mollissima is an important woody crop; however, soil alkalization, a common environmental stressor, limits the sustainable development of its agricultural ecology. The evolution of the PRX gene family and its regulatory mechanisms under alkaline stress in this species remain unclear. In the Castanea mollissima genome, 98 CmPRX genes were identified, distributed unevenly across 12 chromosomes and classified into eight subfamilies. Tandem duplication was the primary driver of the expansion of this gene family. Under alkaline stress, key physiological indicators (SOD and CAT activities, MDA content) in leaves changed significantly, reflecting the plant’s physiological response and adaptive potential under such conditions. Integration of transcriptomic and physiological data revealed highly differentiated expression patterns among CmPRX members. The reliability of the RNA-seq data was validated by RT-qPCR analysis. Weighted Gene Co-expression Network Analysis (WGCNA) identified specific modules significantly correlated with antioxidant enzyme activities, suggesting a pivotal role for this gene family in regulating oxidative balance. This study systematically clarifies the evolutionary characteristics of the CmPRX gene family and its expression regulatory network under alkaline stress. The findings provide a theoretical basis and candidate gene resources for improving alkaline tolerance in C. mollissima through genetic breeding, and offer important insights for selecting stress-tolerant varieties in regions affected by soil alkalization.