Advances in Poultry RNA-Omics Research: Technologies, RNA Information Layers, and Applications in Complex Traits

RNA-omics technologies have expanded poultry transcriptome research beyond tissue-level gene abundance. They now resolve intact transcripts, RNA chemical modifications, cellular origins, and spatial locations. This review centers on a core question: what specific, previously inaccessible RNA information does each RNA-omics technology provide? Based on their primary measurement targets, we categorize these technologies into four groups: bulk transcriptome and small RNA sequencing for analyzing gene expression and regulatory RNA networks; long-read and direct RNA sequencing for resolving transcript isoforms; epitranscriptomic methods for detecting RNA modifications; and single-cell and spatial transcriptomics for identifying the cellular origins and spatial distributions of signals. Methods for resolving RNA structure, RNA-protein interactions, and translation status (e.g., structure probing, CLIP-type mapping, and ribosome profiling) remain in their infancy in poultry, leaving translation and RNA-protein regulation largely unmeasured in tissues such as the oviduct, the lipogenic liver and nucleated erythrocytes. For each category, we discuss its direct measurement targets and primary outputs, the additional information it provides compared to established methods, representative applications in poultry, and its inherent limitations. Building on this framework, we discuss how to select and combine technologies based on specific research questions and summarize their applications in studies of production performance and product quality, reproduction, and health and resilience. Different technologies measure distinct types of RNA features and are not simply interchangeable. Future research must place greater emphasis on matching technologies to scientific questions, integrating complementary data, and improving three foundations: the annotation of poultry transcripts and non-coding RNAs, standardized analytical pipelines, and functional validation systems.