Dissecting resistance mechanisms to Agroathelia rolfsii in peanut (Arachis hypogaea L.) through comparative RNA-Seq profiling of resistant and susceptible genotypes

Abstract Stem rot, caused by the fungal pathogen Agroathelia rolfsii , is a devastating disease in peanut ( Arachis hypogaea L.), resulting in substantial global agricultural losses. This study employed RNA sequencing to unravel the molecular mechanisms of resistance by analysing the gene expression profiles of a resistant peanut genotype (Georgia-03 L) and a susceptible genotype (Valencia C) under normal and infected conditions. From the sequencing data, 405.9 million high-quality reads were successfully mapped to the A. hypogaea reference genome, achieving an average mapping rate of 97%. The alignment showed that out of the 67,124 annotated genes in the Tifrunner genome, 49,598 were expressed in at least one sample. In the resistant genotype, key defense-related genes, including receptor-like kinases, NBS-LRR resistance genes, and transcription factors such as MYB and zinc finger proteins, were strongly induced upon infection in G03L. Weighted Gene Co-expression Network Analysis (WGCNA) identified a coexpression gene module which associated with resistance and enriched with the genes involved in oxidative stress response, secondary metabolism, and cell wall reinforcement. In contrast, the susceptible genotype displayed a limited activation of these defense pathways, emphasizing its vulnerability to A. rolfsii . Functional annotation highlighted critical pathways, such as oxidoreductase activity, glutathione metabolism, and peroxidase-mediated responses, as pivotal to the resistance mechanisms. These findings provide valuable insights into the molecular basis of stem rot resistance in peanuts, offering a foundation for breeding or genetic engineering approaches to enhance disease resistance in susceptible cultivars.