Functional genomics and proteomics in broiler chickens: an integrative framework for growth, immune competence, and stress adaptation

Abstract Functional genomics and proteomics have become key to understanding the biological mechanisms behind growth, health, and resilience in modern broiler chickens. Intensive genetic selection for rapid growth and feed efficiency has led to significant productivity improvements. However, physiological limits are related to muscle integrity, immune function, metabolic balance, and stress tolerance. This narrative review summarizes recent advances in functional genomics and proteomics as applied to broiler chickens, focusing on how these approaches help explain molecular regulation at both the transcriptional and protein levels. Transcriptomic studies have provided important insights into gene expression patterns that control skeletal muscle development, immune responses, and adaptation to environmental and nutritional challenges. Meanwhile, proteomic analyses show that protein levels, modifications, and turnover often differ from transcript-level patterns, emphasizing additional regulatory layers that genomics alone cannot capture. Combining functional genomics and proteomics has become essential for linking genetic potential to phenotypes in fast-growing broilers. This review explores how these omics approaches have improved understanding of key biological areas, including muscle growth and meat quality, immune function and host–pathogen interactions, and molecular responses to environmental and nutritional stressors. Special attention is given to regulatory networks that coordinate metabolism, stress response, and immunity under commercial production conditions. The review also highlights current challenges related to annotation, standardization, and data integration, as well as new opportunities presented by single-cell, spatial, and longitudinal multi-omics technologies. Overall, functional genomics and proteomics offer a scientific foundation for developing precise nutrition strategies, informed breeding programs, and management practices aimed at balancing productivity with robustness, welfare, and sustainability in modern broiler production systems.