Comparative genomic characterization of indigenous fat-tailed Akkaraman sheep with local and transboundary sheep breeds

The domestic sheep with over 1200 breeds descended from those early domesticated animals that are bred for a variety of resources such as meat, milk and wool. Akkaraman, a fat-tailed indigenous sheep breed of Türkiye, is widespread throughout Central Anatolia, with the largest indigenous sheep population. Assessing the genetic diversity and genomic structure of animal breeds is among the key contributors to deciphering adaptation to environmental extremes and constructing efficient genetic improvement strategies. Therefore, this study aimed to characterize the genome of Akkaraman breed against various world-renowned transboundary sheep and indigenous sheep with fat and thin tails. Genetic similarities and differences between those breeds have been displayed by estimating and comparing various genetic diversity indices, linkage disequilibrium (LD) estimates and fixation index (F_ST), runs of homozygosity (ROH) as well as PCA and neighbour-joining tree analysis. Akkaraman sheep were observed to form a cluster alongside Moghani, Karakas, Tibetan and Cyprus Fat Tail sheep, which are primarily the sole representatives of fat-tailed sheep in the study. This clustering was evident in both the PCA and neighbour-joining tree analysis. The Akkaraman sheep was also observed to have the lowest genomic inbreeding and one of the lowest numbers of ROHs, which might also indicate that the breed has not been exposed to historical intensive selection pressure, inbred mating or a massive population bottleneck that might leave strong marks of genomic homozygosity. The results improve our understanding of the genetic diversity in Akkaraman sheep in comparison with certain mainstream sheep breeds as well as those indigenous breeds from around the world. Additionally, findings will also provide valuable insights to perform further GWAS effectively by considering population structure, diversity and LD patterns observed among the breeds while providing practical knowledge that will contribute to designing efficient and successful genome-based selection programmes for worldwide sheep production systems.