Diversity of D-loop mitochondrial DNA (mtDNA) sequence in Bali and Sumba Ongole cattle breeds

Abstract

This study aimed to investigate the diversity of the complete sequence of D-loop mitochondrial DNA (mtDNA) in Bali and Sumba Ongole (SO) cattlebreeds. A total of 24 blood samples were collected from Bali cattle (19 heads) and SO cattle (5 heads), and were extracted and then analyzed to obtain the sequence of D-loop mt DNA.Multiple alignments of the whole sequence of D-loop mtDNA were determined using clustal W. Genetic distance was calculated using a p-distance method, while the genetic tree was constructed using neighbor-joining (NJ) based on MEGA 6. Haplotype number, haplotype diversity (Hd) and nucleotide diversity (Pi) were analyzed using DnaSP version 6. As a result, the sequence of D-loop mtDNA in Bali cattle (921-1119 bp) and SO cattle (913 bp) was reported to have 8 and 4 haplotypes. Hd and Pi of Bali cattle reached 0.625±0.139 and 0.0266±0.0145, respectively, which wwere different from that of SO cattle, namely 0.900±0.1610 and 0.0064±0.0015, respectively. Specifically, we found 22 bp-repetitive nucleotide in Bali cattle, existing 3-9 times with a length of 66-198 bp present in D-loop mtDNA. This unique feature did not exist in SO cattle. Genetic distance and genetic tree determined according to sequence in hypervariability (HV-1) region of D-loop mtDNA (166 bp) resulted in satisfied separation, successfully classifying Bos javanicus, Bos indicus, and Bos taurus cluster.

Phylogenetic tree analysis for Bali Cattle based on partial sequence 16S rRNA Mitochondrial DNA

“…The nucleotide composition of A-T was higher than G-C. This result was conducted well with the previous study in Bali cattle, including d-loop sequenced [6,7], Cyt-b sequenced [8,9], COI [10]. This finding is also consistent in another breed of cattle.…”

“…No reports about 16S rRNA sequenced in Bali cattle. Most phylogenetic studies in Bali cattle using d-loop [6,7], Cyt-b sequenced [8,9], COI [10,11]. Thus, the objective of this research was to identified a phylogenetic tree among Bali cattle and four cattle breeds (Bos indicus, Bos taurus, Bos frontalis, and Bos grunniens) based on partial sequenced of 16S rRNA gene.…”

Population diversity, admixture, and demographic trend of the Sumba Ongole cattle based on genomic data

“…A thorough understanding of livestock diversity and population structure is required for maintaining genetic variation and is crucial for developing future breeding strategies, and the use of molecular technology for this purpose is gaining popularity [ 7 ]. Previously, the genetic diversity of SO cattle has been investigated through various analyses utilizing low-density microsatellite markers and mitochondrial DNA markers [ 8 , 9 ]. The revolution in molecular approach and the increasing availability of a large number genome-wide single nucleotide polymorphisms (SNPs) of animals have transformed them into the most important markers, and they are now intended to be used for genetic studies [ 10 , 11 ].…”

​Elucidation of Genetic Divergence among Cattle Breeds of Tamil Nadu in Mitochondrial Genome

“…Maternally inherited mitochondrial DNA (mtDNA) has been extensively used to determine the genetic variation and phylogenetic relationships of domestic cattle, but related studies have been mostly restricted to the short hypervariable region which makes it impossible to clearly distinguish between some important ancient branches within the phylogenetic tree. To date, most mtDNA studies have focused on the control region (D-loop) (Jakaria et al 2019). Therefore, the present study aims in including the additional information on the matrilineal genetic diversity and phylogenetic status of the cattle breeds of Tamil Nadu using mitochondrial DNA (mtDNA) sequence data obtained from the whole genome sequencing.…”