Genome-wide analysis of conserved and novel miRNAs in mango mesocarp reveals early regulatory networks involved in postharvest heat stress response

MicroRNAs (miRNAs) are key post-transcriptional regulators involved in plant development and stress responses. Although extensively studied in model species, their functional roles remain largely unexplored in non-model fruits, such as mango (Mangifera indica L.). In this study, we present, to our knowledge, the first genome-wide analysis of miRNAs in mango mesocarp under postharvest heat stress induced by hot water treatment (HWT), a widely used quarantine method. Using small RNA sequencing (sRNA-seq), we identified 90 miRNAs distributed across 27 families. Phylogenetic analysis revealed evolutionary trajectories shaped by whole-genome duplication. Most miRNAs were predicted to target transcription factors and regulators involved in growth and hormone signaling. Differential expression profiling across multiple time points post-HWT identified miR168, miR319, and miR482 as early heat-responsive miRNAs. Stem-loop and RT-qPCR validation revealed regulatory modules, including the miR168/AGO1 feedback loop and the miR319/TCP4-GAMYB axis, involved in ROS homeostasis and thermotolerance. In addition, a transient heterologous expression assay in Nicotiana benthamiana demonstrated the functional repression of MiTCP4 by miR319. Additionally, a putative interaction between miR482 and a long non-coding RNA (lncRNA) was uncovered, suggesting a potential coordination of phasiRNA generation during heat stress. These findings provide new insights into miRNA-mediated regulation in mango, highlighting both coding and non-coding networks, and lay the groundwork for future functional studies and the development of miRNA-based tools to improve thermotolerance and fruit quality.