Mitochondrial and Retroviral Markers Reveal High Genetic Diversity and Regional Structure in the Lebanese Awassi Sheep

The Awassi is a native sheep breed of Lebanon with high historical and economic value. Despite its importance, its genetic background has not been characterized, leaving limited understanding of its origins, diversity, and regional connections. This study aimed to characterize the genetic diversity and population structure of Awassi sheep from Lebanon and neighboring Syria using two complementary genetic systems that trace distinct evolutionary histories: maternal mitochondrial DNA and insertional polymorphisms of endogenous Jaagsiekte sheep retroviruses. Genetic analyses were conducted on two hundred seventy-seven animals. Sequencing of a one thousand thirty-four base pair fragment of the mitochondrial cytochrome b gene identified eighty-six maternal haplotypes that clustered into four haplogroups (A, B, C, and E). Maternal haplotype diversity was high, and most individuals belonged to haplogroups A and B, indicating contributions from both western and eastern maternal lineages. Retroviral insertion profiling showed that the retroviral type carrying only endogenous Jaagsiekte sheep retrovirus element eighteen was predominant. A Mediterranean retroviral type carrying both endogenous Jaagsiekte sheep retrovirus eighteen and seven was also present, especially in coastal flocks, suggesting ancient gene flow through maritime trade. Other retroviral combinations were rare. Analysis of endogenous Jaagsiekte sheep retrovirus six revealed a high frequency of solo long terminal repeat alleles, indicating an ancient recombination event. Approximately half of the animals were heterozygous for this allele and some homozygous. No pre-integration alleles were detected, confirming fixation of endogenous Jaagsiekte sheep retrovirus six in domestic sheep. Lebanese Awassi sheep exhibit substantial genetic diversity across both maternal and retroviral systems, reflecting a complex population history shaped by multiple lineages and regional exchanges. This study provides the first comprehensive genetic characterization of this native breed and contributes to broader understanding of sheep domestication in the Middle East, while supporting evidence-based conservation of this valuable genetic resource.