Unveiling genomic diversity and population structure in three Anatolian goats at genome-wide level

Goats, domesticated around 10,000 years ago, have played a vital role in human civilization, particularly in developing regions where they are valued for their economic and ecological versatility. T & uuml;rkiye, acting as a geographic bridge between Asia and Europe, is home to significant native goat populations, including Hair (HAI), Honaml & imath; (HNM), and Kabakulak (KBK) goats. Despite their importance, limited genetic research has been conducted, especially on KBK, which has historically been classified as a sub-variety of HAI. This study is the first to apply double-digest restriction-site associated DNA sequencing (ddRADseq) to explore the genomic diversity and population structure of these breeds, analyzing 309,342 single nucleotide polymorphisms (SNPs) from 481 individuals. Genetic diversity parameters highlighted notable differences among the breeds. HAI exhibited the highest observed heterozygosity (HO = 0.307) and nucleotide diversity (pi = 0.281), whereas KBK displayed the lowest values (HO = 0.301 and pi = 0.278). Principal component analysis (PCA) and ADMIXTURE algorithm identified KBK as a separate genetic cluster, distinct from the overlapping HAI and HNM populations. Pairwise genetic differentiation (FST) values confirmed KBK's genetic distinctiveness. Effective population size (Ne) estimates showed a historical decline across all breeds, with HAI maintaining the largest values. Linkage disequilibrium (LD) decay patterns further highlighted higher genetic diversity in HAI. These findings underline the need for conservation strategies to preserve KBK's genetic composition. This study provides insights into the genetic diversity of Turkish native goats, offering a foundation for sustainable breeding programs and contributing important data to livestock genetics research.