Omics Approaches to Unveil Biotic Stress Responses in Olive: Current Knowledge and Future

Olive (Olea europaea) is a perennial crop of major economic, cultural, and ecological importance in the Mediterranean basin and worldwide, yet its productivity and sustainability are increasingly constrained by diverse pathogens, including fungi, bacteria, and viruses. The primary objective of this review is to critically evaluate how recent omics advances have improved our understanding of olive immune regulation under biotic stress, and to clarify why an integrative systems-level multi-omics perspective is essential for developing durable disease management strategies. By synthesizing genomic, transcriptomic, and emerging proteomic, microbiomics and metabolomic studies, we show that olive defense relies on tightly coordinated transcriptional reprogramming, hormone crosstalk, metabolic remodelling, and structural barriers, within a multilayered immune framework, supported by expanding genomic resources and resistance-associated loci in cultivated and wild germplasm. However, the review also identifies major limitations that currently hinder progress, including a predominant transcript-centric focus, limited proteomic, microbiomics and metabolomic depth, insufficient attention to post-translational and epigenomic regulation, underdeveloped pan-genomic frameworks, and scarce functional validation using genome-editing approaches. We conclude that integrating multi-layered omics with functional genomics and pan-genomics is crucial for translating molecular insights into resilient cultivars and sustainable disease management, and we outline key priority directions for future research and breeding applications.