Unveiling maternal lineages of Sopas sheep: insights from complete mitochondrial DNA cytochrome b (Cyt b) and displacement loop (D-loop) analyses.

Sopas sheep, a native genetic resource from Banyuwangi, Indonesia, are increasingly recognized as a potential distinct local breed; however, their maternal genetic diversity remains poorly characterized. This study aimed to analyze the genetic diversity and phylogenetic relationships of Sopas sheep using complete mitochondrial DNA Cyt b and D-loop sequences. Ten blood samples were collected and analyzed by PCR amplification and sequencing, followed by alignment, haplotype and nucleotide diversity estimation, genetic distance analysis, and phylogenetic reconstruction using neighbor-joining and UPGMA methods. The Cyt b gene showed high conservation (π = 0.00070; Hd = 0.3778), suggesting maternal uniformity and recent ancestry, whereas the D-loop region revealed higher variability (π = 0.00934; Hd = 0.8444), identifying six haplotypes among the ten samples and indicating ongoing diversification. Phylogenetic and genetic distance analyses consistently clustered Sopas sheep with Indonesian local breeds, including Wonosobo, Sapudi, and Javanese Fat-Tailed sheep, underscoring their integration into the national genetic pool. Notably, nine animals were grouped within haplogroup B, while one belonged to haplogroup A, a lineage common in Asian sheep, reflecting multiple maternal origins and historical introductions via trade and migration. These findings demonstrate that Sopas sheep are both conserved and genetically diverse, with dual maternal lineages that strengthen their uniqueness. It is concluded that Sopas sheep represent an important genetic resource requiring conservation and structured breeding to prevent genetic erosion, while future integration of mitochondrial and nuclear markers is recommended to ensure their long-term sustainability.