Genetic Diversity and Phylogenetic Relationships of Seven Dairy Goat Breeds in Yogyakarta and Central Java Based on Cytochrome B Gene

Indonesia is endowed with numerous goat breeds, including meat-type, dual-purpose, and dairy goats. Previous studies have shown that some goat breeds are at risk of extinction, while the level of extinction risk for most Indonesian dairy goat breeds remain unknown. Moreover, the characterizations of Indonesian dairy goat breeds have been dominated by phenotypic descriptions with limited molecular data analysis. This study was conducted to explore the genetic diversity and phylogenetic relationship of seven dairy goat breeds found in Yogyakarta and Central Java, which included Saanen, British Alpine, Bligon, Anglo Nubian, Toggenburg, Nigerian dwarf, and the crossbred of Anglo Nubian with PE. DNA was extracted from blood samples taken from 31 goats. A 430 bp segment of the mitochondrial cytochrome b (cyt b) gene was amplified and sequenced, followed by aligning with reference sequences obtained from GenBank and then phylogenetic and genetic diversity analyses. Phylogenetic tree constructed showed two main clades where Nigerian dwarf goat was in separate clade from other dairy breeds. Three hypervariable sites, five polymorphic sites, five number of mutations and eight number of haplotypes were found across all samples suggesting low to moderate genetic differentiation among the breeds. The overall haplotype diversity and nucleotide diversity were 0.716±0.058 and 0.00251±0.00035, respectively while genetic distances among breeds ranged from 0.0 to 0.0038. The AMOVA results showed 82.17 of genetic variation was found within breeds, while 17.83 of the genetic variation was found among breeds. The revealed low to moderate genetic diversity among seven dairy goats breeds in this study indicates a narrow genetic base and high genetic homogeneity which may reduce adaptability and increase extinction risk. The findings highlight the urgent need for structured breeding programs and increased farmers awareness to conserve genetic resources. © 2026, Gadjah Mada University. All rights reserved.