Preliminary Study on Phylogenetic Analysis of Sakub Sheep from Brebes Regency Based on the Mitochondrial DNA (mtDNA) Displacement Loop (D-Loop) Gene Sequence
Preliminary Study on Phylogenetic Analysis of Sakub Sheep from Brebes Regency Based on the Mitochondrial DNA (mtDNA) Displacement Loop (D-Loop) Gene Sequence
Rana Ayuningtyas Adhi Puspita1, Alek Ibrahim2, Endang Tri Margawati3, Ismu Subroto4, Zaenab Nurul Jannah5, Panjono5, Krisna Noli Andrian6, Medania Purwaningrum6, Aris Haryanto6*
ABSTRACT
The mitochondrial DNA (mtDNA) Displacement Loop (D-Loop) gene is commonly used in genetic studies due to its variability and ability to provide insights into phylogenetic relationships. Sakub sheep, a local Indonesian breed from Brebes Regency in Central Java, have not yet been studied using D-Loop gene sequences to determine phylogenetic relationships. This research aims to analyze the genetic relationships of Sakub sheep with other breeds and identify their haplogroup. DNA isolates from Sakub sheep were amplified using specific primers (Alek-DLF 5’-GAAGAAGCTATAGCCCCACT-3’ and Alek-DLR 5’-GATTCGAAGGGCGTTACT-3’), sequenced, and analyzed with MEGA software. Comparative data was sourced from NCBI GenBank. Sequence alignment revealed 1180 base pairs, with 1131 monomorphic sites, 50 polymorphic sites, 11 segregating sites, and 39 parsimony-informative sites. Genetic distances among Sakub samples ranged from 0.000 to 0.039, indicating a close phylogenetic relationship among individuals. Two samples (SKB.4 and SKB.8) were classified under haplogroup A, while six (SKB.1, SKB.2, SKB.3, SKB.5, SKB.6, SKB.7) were under haplogroup B. The findings suggest that Sakub sheep predominantly belong to haplogroup B and share close phylogenetic relationships with other local Indonesian breeds as well as international breeds such as Merino, Suffolk, and Texel.
Keywords | D-Loop gene, Phylogenetic, Polymerase chain reaction (PCR), Sakub sheep
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July 2025
Adv. Anim. Vet. Sci., Vol. 13, Iss. 7,
