Transcriptomic Comparison of Rice lncRNAs in Response to Feeding by Brown Planthopper Populations with Different Virulence

The brown planthopper (BPH) is one of the major rice pests causing significant damage to rice production worldwide, due to its high reproductive capacity and strong migratory ability. A series of BPH-resistant rice varieties have been developed, but the durability of effective resistance is constrained by the evolution of BPH virulence, requiring in-depth insights into resistance mechanisms. In this paper, we used strand-specific lncRNA-seq to characterize the lncRNA regulatory mechanisms on rice response to BPH infestation. Overall, 4321 lncRNAs were identified, 60 of which were significantly upregulated in response to BPH infestation, specifically differing between BPH populations with variable virulence. Differential expression analysis and qRT-PCR validation showed that these lncRNAs are involved in the regulation of several defense pathways, including jasmonic acid signaling and flavonoid biosynthesis, with their distinct roles in resistant and susceptible rice varieties. Notably, lncRNAs like <i>LNC_002533</i> were found to be negatively correlated with flavonoid biosynthesis, suggesting a potential role in modulating rice defense responses. In contrast, <i>LNC_001986</i> and <i>LNC_000397</i> were positively correlated with genes involved in glutathione metabolism, which may be associated with enhanced resistance. These findings highlight the critical regulatory functions of lncRNAs in rice-BPH interactions and provide a molecular framework for improving rice resistance through targeted genetic engineering. This study significantly contributes to functional genomics by elucidating lncRNA-mediated regulatory mechanisms and offers promising avenues for developing durable pest-resistant rice varieties.