Omics Evidence Chains for Complex Traits in Beef Cattle: From Cross-Layer Colocalization to Genetic Evaluation and Application

Multi-omics studies have multiplied associations, but many still lack causal resolution and a clear path to application. We present a practical roadmap built on four sequential steps: first, identify signals from genome-wide association studies; second, confirm these signals through regulatory colocalization and transcriptome-wide association analyses; third, integrate the evidence using network analyses and causal inference; and, fourth, test shortlisted candidates through functional and phenotypic validation. The roadmap is supported by three safeguards that make results reliable and reusable: containerized workflows that ensure end-to-end reproducibility, harmonization across batches with concise minimum-information records, and consistent identifier mapping with quality control across data layers. Across four classes of traits-growth and development, carcass and meat quality, reproduction, and environmental adaptation and resilience-we prioritize signals that remain robust across ancestries and environments, highlight modules with explicit regulatory support, and advance candidates that have already progressed to functional testing. Two application tracks follow from this process: integrating stable candidates into selection indices with context-dependent weighting, and recording and targeting mechanistic nodes for nutritional and management interventions. Taken together, this roadmap improves causal interpretability, strengthens cross-population robustness, and shortens the path from statistical association to genetic evaluation and industry uptake.