Investigating genetic diversity of Indonesian native cattle breeds using mitochondrialDNA 16S rRNA gene

Abstract

This study aimed to estimate the genetic diversity and phylogenetic relationships of Indonesian native and local cattle breeds using 16S rRNA mitochondrial DNA. The study analyzed 93 DNA samples from six cattle breeds. The polymerase chain reaction was conducted using two primer pairs to sequence the complete 16S rRNA gene. The number of the polymorphic site (S), pairwise nucleotide differences (K), haplotype diversity (Hd), and nucleotide diversity (?) were estimated using DnaSP 6 software. PopART v. 1.7 software was employed for the median-joining network analysis, while a neighbor-joining tree was reconstructed based on the Kimura 2-parameter model using MEGA X software. The results revealed 29 haplotypes, 14 in Bali cattle. The haplotype diversity varied from 0.24 ± 0.135 to 0.92 ± 0.084. The overall nucleotide diversity among populations was 0.0190 ± 0.0011. Indonesian native cattle revealed high variability in the 16SrRNA gene sequence. The phylogenetic analysis assigned the Bali cattle as Indonesian native cattle separated from the other cattle breed.