miRNA-Mediated Regulation of Meloidogyne arenaria Responses in Wild Arachis

MicroRNAs (miRNAs) are key post-transcriptional regulators of plant development and stress responses, with many conserved across diverse plant lineages. In this study, we investigated the expression profiles of miRNAs and their corresponding target genes in Arachis stenosperma, a wild peanut relative that exhibits robust resistance to root-knot nematodes (RKN). Small RNA sequencing of nematode-infected roots identified 107 miRNA loci, of which 93 corresponded to conserved miRNA families and 14 represented novel candidates, designated as miRNOVO. Among these, 18 miRNAs belonging to 11 conserved families were identified as differentially expressed (DEMs). Integrated analysis of miRNA and transcriptome data revealed multiple miRNA–mRNA regulatory interactions involving key components of plant defense, including regulators of hormone signaling pathways (e.g., auxin, jasmonic and salicylic acid), cell wall reinforcement, redox regulation, development control and nutrient homeostasis. Remarkably, four immune receptor genes belonging to the nucleotide-binding site leucine-rich repeat (NLR) family displayed inverse expression patterns relative to their regulatory miRNAs, suggesting miRNA-mediated post-transcriptional control during the early stages of nematode infection. These findings reveal both conserved and species-specific miRNA–mRNA modules associated with nematode resistance in A. stenosperma, highlighting promising targets for developing RKN-tolerant peanut cultivars through miRNA-based strategies.