Mapping the Genetic Structure in Chicken Genomes Using SNP Chips: Perspectives on Conservation and Breeding

Abstract

Rapidly increasing global human population has significantly raised the demand for high-quality and sustainable protein sources. In this context, chicken meat has a strategic importance in human nutrition due to its economic production efficiency, high nutritional value, and low environmental footprint. It is anticipated that meeting future protein requirements will largely depend on enhancing productivity and adopting sustainable poultry production systems. Therefore, accurately revealing the genetic potential of local chicken breeds is crucial, not only for increasing productivity but also for maintaining biological diversity. Understanding genetic structure and diversity among chicken breeds is essential for sustainable animal breeding programs and the conservation of local genetic resources. Recently, high-density Single Nucleotide Polymorphism (SNP) chip technologies have emerged as powerful tools for investigating genetic characteristics in chickens. This technology enables simultaneous analysis of thousands of SNPs, facilitating accurate and precise assessments of population structure, inbreeding levels, heterozygosity rates, and genetic differentiation indices (FST). Different SNP chip densities (e.g., 5K, 10K, 50K, and 100K SNP) are available, and their selection depends primarily on research objectives, genetic composition of populations, and budget considerations. These SNP chips offer a broad spectrum of applications, ranging from basic genetic diversity analyses to genome-wide association studies (GWAS). This review focuses on genetic analyses conducted in chickens using SNP chip technology and comprehensively evaluates current literature on comparative genomic profiling of local and commercial breeds. Additionally, it addresses methodological approaches, advantages, and limitations associated with widely-used commercial SNP chips, such as those provided by Illumina and Affymetrix. The strategic role of SNP data in identifying selection signatures, mapping homozygous a critical component not only at the molecular level but also in applied animal breeding policies