Integrative multi-omics and predictive precision systems for poultry meat and egg quality: Mechanisms, applications, and commercial challenges

Abstract

Poultry meat and egg quality result from complex interactions among host genetics, metabolism, nutrition, microbiome ecology, physiology, management practices, and environmental conditions. These multidimensional interactions limit the predictive capacity of conventional phenotype-based approaches and increasingly necessitate systems-level frameworks capable of capturing biological complexity. Recent advances in multi-omics technologies have transformed poultry quality research by enabling integrated analyses of genomic, transcriptomic, proteomic, metabolomic, lipidomic, epigenomic, and microbiome datasets. These approaches have substantially enhanced understanding of the molecular, cellular, physiological, and ecological networks associated with product quality, production efficiency, physiological resilience, and environmental adaptation. Integrated multi-omics analyses, particularly when combined with artificial intelligence and machine-learning approaches, have the potential to identify biologically interpretable biomarkers, candidate mechanistic pathways, and predictive signatures associated with meat and egg quality traits; however, most proposed signatures remain at early stages of validation and require rigorous external testing before commercial deployment. This review synthesizes current advances in omics-driven poultry research and critically evaluates emerging applications in precision nutrition, breeding, health monitoring, environmental adaptation, and sustainable production systems. To provide a unifying biological framework, we propose the Adaptive Systems Theory of Poultry Quality (ASTPQ), which conceptualizes poultry quality as an emergent adaptive phenotype arising from coordinated interactions among mitochondrial function, redox homeostasis, immune competence, metabolic flexibility, physiological resilience, endocrine–immune regulation, and host–microbiome dynamics. Within this conceptual framework, adaptive-system capacity is proposed as the principal integrative mechanism linking molecular regulation with phenotypic quality outcomes across diverse production environments. Despite substantial advances, commercial implementation remains constrained by biological heterogeneity, methodological variability, limited external validation, computational complexity, challenges in data integration, infrastructure requirements, and economic barriers. Current evidence suggests that predictive performance depends less on increasing molecular dimensionality than on developing biologically interpretable, externally validated, economically feasible, and operationally scalable systems. Future progress will likely require integrated precision-production frameworks that combine molecular biomarkers, physiological monitoring, environmental sensing, microbiome-informed interventions, explainable artificial intelligence, and rigorous large-scale field validation to support sustainable, resilient, and commercially applicable poultry production systems.