Genetic diversity and relationship among Indonesian local sheep breeds on Java Island based on mitochondrial cytochrome b gene sequences

Background The cytochrome b (Cyt b) gene is one of the most studied mitochondrial DNA (mtDNA) genes to determine sheep’s genetic profle. This study aimed to determine the genetic diversity and relationships of severalIndonesian local sheep populations on Java Island, Indonesia, based on the mtDNA Cyt b gene sequences. Blood samples were collected from forty-one individual sheep in seven populations of Indonesia local sheep breeds on Java Island (Priangan=6, Garut=6, Batur=7, Wonosobo=5, Javanese Thin-Tailed/JTT=7, Javanese Fat-Tailed/JFT=5, andSapudi=5). DNA extraction was performed on blood samples, and the mtDNA Cyt b gene was amplifed using specifc primers (Alek-CBF: 5’-CAACCCCACCACTTACAA-3’ and Alek-CBR: 5’-CCTTGAGTCTTAGGGAGGTT-3’). The polymerase chain reaction (PCR) products were then sequenced, and data were analyzed using the MEGA version 7.0, DNA SP
version 6.0, and NTSYS-pc version 2.11 software.
Results A total of 1140 bp complete mtDNA Cyt b gene sequences in this study obtained 1134 monomorphic sites
(I), six polymorphic sites (V), one segregation site (S), and fve parsimony informative sites (P) with a nucleotide diversity (Pi), the average number of nucleotide diferences (K), and sequence conservation (SC) were 0.00119, 1.35610,
and 0.9947, respectively. There were six haplotypes consisting of two unique haplotypes and four shared haplotypes with a haplotype diversity (Hd) of 0.5415. The genetic distance within and between populations ranged from 0.0000 to 0.0016 and 0.0000 to 0.0020, respectively. Wonosobo, JFT, and Sapudi sheep have the closest relationship, and then these three breeds were close to JTT sheep, followed by Batur, Priangan, and Garut sheep. Two haplogroups have been found based on the Ovine haplogroup clustering. All Wonosobo, JTT, JFT, Sapudi sheep, and most Batur sheepwere clustered into haplogroup B. In contrast, Garut sheep were mostly clustered into haplogroup A, while Priangan sheep were clustered into both haplogroups with the same percentage. Conclusion Seven Indonesian local sheep breeds on Java Island have a close relationship clustered into two haplogroups, namely haplogroups A and B. Most Indonesian local sheep breeds on Java Island in this study were clustered into haplogroup B, except for Garut and Priangan sheep.