Genome-Wide Identification and Expression Analysis of the Heavy-Metal ATPase (HMA) Gene Family Reveal Their Correlation with Copper and Cadmium Stress Adaptation in Stevia rebaudiana

Heavy-metal ATPase (HMA) is widely involved in the absorption and transport of metal elements, including copper, zinc, and cadmium in plants. Although the characterization of HMA has been conducted in several plants, the research on the HMA gene in Stevia rebaudiana remains limited. In this study, twelve SrHMA genes were identified, encoding stable proteins mostly localized to the plasma membrane and possessing conserved E1-E2_ATPase and hydrolase domains, with one to three N-terminal HMA domains. Phylogenetic analysis classified them into two subfamilies (Zn/Co/Cd/Pb and Cu/Ag P1B-ATPases). The genes are unevenly distributed across five chromosomes, with two segmental duplication events and an independent genome duplication event specific to dicots, and their promoters harbor abundant stress-responsive elements. Expression profiling under copper and cadmium stresses showed distinct tissue specificity: cadmium stress upregulated most genes in roots but suppressed them in leaves, whereas copper stress upregulated all genes in leaves and half of the genes in roots. This study represents the first systematic analysis of the SrHMA gene family, revealing its potential involvement in heavy-metal stress responses and providing candidate genes for future functional characterization and breeding of S. rebaudiana varieties with enhanced metal tolerance.