Identification and analysis of microRNAs responsible for brown planthopper resistance in BPH14 and BPH15 pyramiding rice

Rice farming faces a significant challenge from the brown planthopper (BPH), a destructive pest that threatens crop yields. Developing BPH-resistant rice varieties is critical for ensuring food security. The pyramiding of BPH resistance genes, BPH14 and BPH15, has proven effective in providing protection in elite rice strains. MicroRNAs (miRNAs) play a pivotal role in plant defense by fine-tuning resistance responses through the modulation of genes involved in various signaling pathways and metabolic processes. B1415, the pyramiding line containing BPH14 and BPH15, exhibits stronger BPH resistance compared to its recurrent parent, Wushansimiao, without affecting other important agronomic traits. However, the molecular basis underlying the resistance conferred by the BPH14/BPH15 pyramiding rice remains largely unclear, particularly with respect to the potential regulatory role of miRNAs. Studying miRNAs in resistance gene pyramiding lines like B1415 is essential for advancing rice breeding efforts, as such research can uncover regulatory networks that enhance pest resistance and identify miRNA-mRNA interactions as potential targets for genetic manipulation. The study investigated miRNA levels in B1415 and their recurrent parent (RP) under BPH infestation employing high-throughput sequencing and revealed 136 differentially expressed miRNAs (DEMs) among 550 known miRNAs. An integrated analysis highlighted that 587 miRNA-mRNA pairs linking 95 DEMs to 537 targeted genes were enriched in phenylpropanoid and lignin metabolism, circadian rhythms, and amino acid metabolism. The candidate DEMs, miR172d-3p, and miR396 family members were identified as negative regulators to decrease their target genes Os06g0708700 (encoding a nodulin-like protein) and Os11g0129700 (encoding an AP2 domain transcription factor), suggesting their key roles in rice against BPH. Our investigation provides the first insights into miRNA-mediated defense mechanisms in the B1415. Identifying miRNAs and their target mRNAs in BPH resistance opens a new avenue for rice breeding programs, offering potential targets for improving pest resistance. Understanding these molecular interactions paves the way for developing more resistant rice cultivars, thereby contributing to sustainable rice production and food security.