Advances in functional genomics of major rice pests and pathogens and their molecular interactions with the host: A...

Rice, a staple crop for billions, faces persistent threats from pests and pathogens jeopardizing global food security. Functional genomics and multi-omics approaches have revealed complex immune strategies in rice, including NLR receptor-mediated resistance, transcriptional regulation, and emerging roles of non-coding RNAs such as long noncoding RNAs, and circular RNAs. Novel mechanisms-such as effector-triggered autophagic degradation (e.g., BISP-BPH14) and circular RNA-derived defense peptides-highlight the multilayered nature of rice immune responses. However, field application of these findings is challenged by effector variability, incomplete understanding of signal crosstalk, and the trade-off between resistance and development. Many resistance loci are suppressed in susceptible backgrounds, indicating a pivotal role for epigenetic regulators and susceptibility genes. Moreover, synergistic haplotypes and resistance modules, rather than single genes, may underlie durable field resistance. Future priorities should include: (1) functional validation of resistance elements under agroecological variation; (2) dissection of resistance-susceptibility and hormone signaling crosstalk; and (3) haplotype-based trait assembly in breeding pipelines. Integrating artificial intelligence, synthetic biology, and nanotechnology will accelerate the design of broad-spectrum immune receptors, multiplex CRISPR-based editing platforms, and climate-resilient cultivars. Embracing a systems-level strategy of "smart sensing, dynamic regulation, and ecological equilibrium" will enable precision management of rice pests and diseases, paving the way toward sustainable crop production.