Genome-wide comparative analysis of variability and population structure between autochthonous Turkish chicken breeds and commercial hybrid lines

Next-generation sequencing (NGS) technologies have revolutionized livestock genomics by enabling rapid, high-resolution genotyping of local populations with thousands of single nucleotide polymorphisms (SNPs), offering unprecedented accuracy and cost efficiency. This study presents the first comprehensive genomic assessment of the Denizli (DNZ) and Gerze (GRZ) chicken breeds, comparing them to commercial broiler and layer hybrid lines using the double digest restriction-site associated DNA sequencing (ddRADseq) technique. A total of 94,208 bi-allelic SNPs were common between DNZ and GRZ, while 33,284 SNPs were retained among all populations after the quality filtering process. Genetic diversity parameters were higher in native Turkish chicken breeds compared to hybrid lines in which minor allele frequency (MAF) was higher than 0.3 in DNZ and GRZ while it was lower than this value in commercial hybrid lines. Notably, DNZ displayed the highest observed (0.386) and expected (0.375) heterozygosity, whereas the broiler hybrid line showed the lowest heterozygosity (0.254), suggesting inbreeding depression (FIS = 0.241). The negative inbreeding coefficient values occurring due to random mating were observed in DNZ and GRZ chicken breeds, while this value was estimated at 0.118 in the layer hybrid line. Population structure analyses such as principal component analyses (PCA), genetic distance-based neighbor-joining (NJ) tree, ADMIXTURE, and TreeMix algorithm revealed that DNZ and GRZ were genetically distinct from both each other and commercial hybrid lines. The results of this study confirm that comprehensive conservation strategies are efficient approaches to keeping genetic variability at an optimal level without inbreeding. Moreover, this study demonstrates the efficacy of ddRADseq in generating high-throughput genotypic data, providing a cost-effective framework for genomic diversity and population structure studies in indigenous chicken breeds.