نوع مقاله : مقاله پژوهشی
عنوان مقاله English
نویسندگان English
Introduction
Intense artificial selection and long-term breeding programs in broiler chickens have substantially improved economically important traits such as growth rate, feed efficiency, and carcass quality. However, these breeding practices have also led to distinct patterns of genetic variation and the formation of genomic regions under selection. Such regions are reflective of selective pressures acting on biological pathways related to growth, energy metabolism, tissue development, and physiological adaptation. Genomic studies have demonstrated that selection signatures are typically associated with local reductions in genetic diversity, elevated linkage disequilibrium, and fixation of favorable alleles in specific genomic regions. In commercial poultry, intensive selection over the past decades has created populations with high production efficiency, but the underlying genomic architecture of these improvements remains incompletely understood. It is expected that genomic analyses can reveal selection signatures that correspond to traits targeted by breeding programs, providing insight into the molecular mechanisms governing growth, metabolism, immunity, and stress resilience. Despite the importance of this topic, comprehensive genomic information on selection patterns and population structure is limited for many commercial broiler lines. Therefore, this study aimed to i) investigate the genetic structure of several commercial broiler populations, ii) identify genomic regions under recent and population-differentiated selection, and iii) functionally characterize candidate genes associated with production and physiological traits.
Materials and Methods
Whole-genome sequencing data from 29 broiler chickens, representing three commercial populations American, French, and Ross 308, were analyzed. Sequence reads were aligned to the chicken reference genome, and single nucleotide polymorphism (SNPs) were extracted. Quality control, filtering, and phasing were applied to generate high-confidence variant datasets. Population genetic structure was evaluated using principal component analysis (PCA), phylogenetic reconstruction, and model-based clustering approaches. To detect selection signatures, two complementary methods were employed: the within population integrated haplotype score iHS and the between two differential populations Rsb statistic. The iHS analysis enables detection of recent selection within populations, while Rsb identifies genomic regions showing differentiated selection between populations with distinct breeding histories. Candidate genes located within these regions were extracted, followed by functional annotation and pathway enrichment analyses to interpret their biological relevance.
Results and Discussion
Population structure analyses revealed clear genetic differentiation among the three broiler lines, likely reflecting differences in breeding history, composition of ancestral lines, and selection intensity. This observation aligns with previous studies demonstrating that long-term breeding programs can shape genetic variation and divergence among commercial poultry populations. Selection signature analyses identified multiple genomic regions harboring genes associated with growth, energy metabolism, lipid regulation, muscle tissue development, and immunity. Identified as a common candidate gene across multiple populations, OSBPL8 plays a central role in lipid metabolism and energy homeostasis. Functional studies have linked OSBPL8 to regulation of lipid transport and growth-related metabolic pathways, indicating its potential contribution to rapid growth and feed efficiency in broilers. Functions as a thyroid hormone-binding protein and modulates energy metabolism in muscle tissue. Its regulatory role in thyroid hormone signaling suggests an impact on growth efficiency and metabolic adaptation, which are critical in intensive production systems. Involved in peroxisome biogenesis, PEX14 regulates fatty acid oxidation and cellular lipid metabolism. Selection on this gene may influence energy utilization and overall physiological performance, highlighting the link between organelle function and production traits. Participates in adipocyte proliferation and tissue differentiation. By affecting the development of fat and muscle tissues, ZFPM2 likely contributes to carcass composition and meat quality traits in broilers. In addition to genes directly related to growth and metabolism, several genes associated with tissue development, neural function, and immune response were detected in regions under selection. These findings indicate pleiotropic effects of artificial selection, reflecting the broad impact of breeding programs beyond target production traits. The detection of genes influencing immunity and heat stress is consistent with prior reports showing selection effects on physiological resilience and health-related traits in broiler populations.
Functional enrichment analyses revealed that selected regions are enriched in pathways governing muscle development, energy metabolism, lipid regulation, immune signaling, and neurodevelopment. Such pleiotropic effects suggest that selection for growth and feed efficiency simultaneously impacts multiple biological networks, leading to correlated responses in tissue composition, metabolic adaptation, and physiological performance. The convergence of selection signatures across populations for genes like OSBPL8 highlights conserved targets of breeding programs, whereas population-specific signals reflect differences in breeding strategies and historical selection pressures. Overall, these results indicate that selection signatures in commercial broiler populations are not confined to genes related to rapid growth and feed conversion but extend to molecular pathways involved in tissue development, neural function, and systemic physiological responses. This complexity underscores the integrated nature of genomic responses to selective pressures in modern breeding programs and emphasizes the importance of considering both direct and pleiotropic effects when designing selection strategies.
Conclusion
Commercial broiler lines exhibit distinct genetic structures and contain specific genomic regions under selection. The candidate genes identified in this study are primarily involved in growth regulation, energy metabolism, muscle tissue development, and immune response. Identification and functional characterization of these regions can facilitate genomic selection strategies aimed at improving production efficiency, enhancing physiological resilience, and increasing the sustainability of poultry systems. Furthermore, understanding the pleiotropic effects of selection provides a framework for more precise utilization of genetic diversity in commercial populations and may guide the development of breeding programs that optimize complex traits, simultaneously.
کلیدواژهها English
