This study is the first whole-genome sequencing study of Yeonsan Ogye Black chicken(Korean indigenous chicken). we identify the nucleotide diversity, linkage disequilibrium pattern, phylogenetic tree analysis, genetic differentiation, admixture analysis, and genome-wide selection analysis across the 188 chickens from 13 populations. We identified the selection signature of OGYE. Our results showed that the OGYE preserved unique genetic characteristics, both phenotypic and genotypic, distinguished from other chicken breeds. Importantly, we identified RNASEL, BRIP1, HSP90AA1, and TLR4 gene regions as essential for promoting the innate immune system, while the SPP1 gene might be essential for developing eggshells in OGYE. Together, our result provides novel insights into the chicken breeding program to manage risk and vulnerability through the indigenous animal genetic resource and facilitate the conservation of OGYE.. Comparative genomics and selection analysis of Yeonsan Ogye Black chic

Yeonsan Ogye (OGYE; Gallus gallus domesticus) is one of the rare indigenous chicken breeds habiting in the Korean Peninsula. As a unique morphological feature, the OGYE breed has entirely black plumage, skin, eyes, and beak, including black internal organs. Despite these unique features, the OGYE population is declining without much in-depth research into their genomes. From this perspective, this study compared the whole genome of the OGYE breed with a total of 13 breeds, including their ancestral, commercial, other indigenous breeds. Our PCA results showed that the genetic variation separates the OGYE and Korean Native Chicken(KNC) breeds. Also, the admixture of OGYE distinguished itself from other chicken breeds. As a result, OGYE have accumulated rare phenotypic and genotypic characteristics underlying environmental pressure and artificial selection. Based on the selection analysis, the OGYE showed the selection signature for eggshell thickness and immune response. For example, regions harboring SPP1 might be crucial for developing the eggshell of OGYE chickens, while RNASEL, BRIP1, HSP90AA1, and TLR4 might be essential for the biological immune response. Importantly, Our results can further understand Korean indigenous chicken. It is valuable for us to understand population dynamics and the evolutionary adaptation of chicken breeds.