Drought is a major environmental constraint limiting global peanut productivity. Wild peanut species, characterized by greater genetic diversity, represent valuable resources for improving drought resilience in cultivated peanut. However, the molecular mechanisms underpinning drought tolerance in wild peanut species remain largely unexplored. This study evaluated the drought tolerance of three wild-type peanut accessions from two different species, Arachis dardani GK12946, Arachis dardani V7215, and Arachis ipaënsis K30076. Physiological measurements such as fresh weight and dry weight revealed statistically non-significant differences between drought-stressed and well-watered conditions, indicating strong inherent drought tolerance. Transcriptome analysis revealed that 3272, 3648, and 1181 genes in leaf samples of A. dardani GK12946, A. dardani V7215, and A. ipaënsis K30076 were differentially expressed, respectively. In root samples, 3014, 3472, and 2033 genes were differentially expressed in the same accessions. Notably, differentially expressed genes (DEGs) and set intersection (Venn) analysis suggests A. dardani V7215 exhibited the highest number of DEGs (1155) uniquely expressed in leaves, and 899 DEGs uniquely expressed in roots, suggesting accession-specific gene expression. Gene Ontology enrichment revealed that upregulated genes were associated with abiotic stress responses, temperature stimulus, heat stress, and DNA-binding transcription factor activity. Co-expression network analysis using WGCNA identified key drought-responsive modules, enriched for GO terms like stress regulation, protein folding, as well as GST family amino acid metabolic processes. Overall, this study provides comprehensive insights into the molecular basis of drought tolerance in wild peanut accessions. Our findings establish a valuable resource for functional genomics and crop improvement under water-limited conditions.
Supplementary Information: The online version contains supplementary material available at 10.1186/s12870-025-07799-7.
Keywords: Arachis dardani; Arachis ipaënsis; Crop improvement, WCGNA (Weighted gene co-expression network analysis); Differentially expressed genes (DEGs); Drought tolerance; Transcriptome analysis; Wild peanut species.