Maternal haplotype diversity and phylogenetic relationships of Damascus, Kilis, Hatay, and Kil goat breeds: insight from mtDNA D-loop sequences in the Fertile Crescent

Abstract. This study focuses on goat populations in Türkiye, a region located within the Fertile Crescent – historically recognized as the birthplace of goat domestication and a crucial source of genetic diversity in livestock species. This study investigates the maternal genetic origins of four prominent goat breeds – Damascus (DMS, n=20), Kilis (KLS, n=21), Hatay (HTY, n=22), and Kil (KIL, n=21) – by analysing 598 base pairs (bp's) of hypervariable region 1 (HV1) within the mitochondrial DNA (mtDNA) displacement loop (D-loop) sequence. The goats utilized in this research were sourced from the “National Breeding Project under Farm Conditions”, a strategic initiative led by the Republic of Türkiye's Ministry of Agriculture and Forestry, General Directorate of Agricultural Research and Policies (TAGEM). The analysis revealed haplotype diversity (Hd) ranging from 0.944 to 0.989 and nucleotide diversity (π) between 0.01734 and 0.02635. Hatay goats exhibited relatively low haplotype diversity (Hd = 0.944±0.028) and nucleotide diversity (π=0.01985±0.00087). Moreover, the presence of shared haplotypes among multiple individuals in Hatay goats indicates a potential genetic bottleneck or prolonged isolation in breeding compared to other breeds. These findings highlight the necessity for conservation strategies aimed at preserving genetic diversity within this population. Haplogroup A was found to be the most prevalent among the studied populations, a distribution that aligns with the global genetic pattern of maternal origins observed in goat populations worldwide. A total of 51 unique haplotypes were identified, with 47 belonging to Haplogroup A and 4 to Haplogroup G, out of the overall 65 haplotypes. A single shared haplotype was identified between Damascus and Kilis goats. For the first time, Hatay goats have been documented as belonging to both Haplogroup A and Haplogroup G. Additionally, this study presents the novel identification of Haplogroup G in Damascus goats. Furthermore, the phylogenetic analysis also supports the emergence of Kilis and Hatay goats. These findings enhance our understanding of caprine genetic diversity and emphasize the necessity of conserving these breeds as crucial genetic resources within the Fertile Crescent region.