Genetic diversity of goats in East Java through analysis of the cytochrome B and cytochrome oxidase I genes in mitochondrial DNA

• Published in: Small ruminant research 2022-04, Vol.209, p.106659, Article 106659
• Main Authors: Suyadi, S., Murtika, I.L., Susilorini, T.E., Septian, W.A., Saputra, F., Furqon, A.
• Format: Article
• Language: English
• Subjects: Evaluation; Haplotype; Indonesian goat; PCR; Sequencing
• ISSN: 0921-4488; 1879-0941
• DOI: 10.1016/j.smallrumres.2022.106659

The aim of this research was to evaluate Kacang, Senduro, PE, Boer, and Saanen goats through the mitochondrial cytochrome B (Cyt B) and cytochrome oxidase I (COI) genes. The Parameter estimates used in the present study were number of haplotypes (NHap), haplotype diversity (Hd), nucleotide diversity (Pi), conserved sites, variable sites, nucleotide composition and genetic distance. A total of 47 samples were used in the current study. Genomic DNA was extracted from blood samples. DNA was amplified using primers designed according to caprine genomic sequence in GenBank (KF952601). The results showed that the Cyt B gene had 64 variable sites and 20 haplotypes. The Hd and Pi values were 0.891 ± 0.032 and 0.00552 ± 0.00375, respectively. There were 29 variable sites and six haplotypes in the partial COI gene. The Hd and Pi values were 0.471 ± 0.058 and 0.00155 ± 0.00152, respectively. In conclusion, the genetic distance among East Java goat populations was close to each other, except for the Saanen goat that has the farthest distance. •Genetic distance in East Java goats can be identified using Cyt B and COI.•Indonesian goats have an ancestral relationship with the Capra hircus and capra aegagrus.•Genetically, the kacang goat was found in almost all the branches in the phylogenetic tree.