Genetic Diversity of Mitochondrial DNA Cytochrome b in Indonesian Native and Local Cattle Populations

Peni Wahyu Prihandini, A Primasari, M Luthfi, J Efendy, D Pamungkas


Information on the genetic diversity of native and local cattle in Indonesia is vital for the development of breeding and conservation strategies. This study was aimed to assess the genetic diversity and phylogenetic relationship of the Indonesian native (Bali) and local [(Donggala, Madura, Sragen, Galekan, Rambon, dan Peranakan Ongole Grade x Bali (POBA)] cattle populations. Genomic DNA was extracted from blood samples (n= 75). Partial sequences of mtDNA cyt b, 464 bp, were amplified using the polymerase chain reaction technique (forward primer: L14735 and reverse primer: H15149). Thirty-four reference sequences of Bos taurus, Bos indicus, and Bos javanicus were included in the phylogenetic analyses. A total of 55 polymorphic sites and 13 haplotypes were observed in the whole breeds. No variable sites of mtDNA cyt b were observed in Galekan (kept in BCRS) and Rambon cattle. Overall haplotype diversity and nucleotide diversity were 0.515 ± 0.070 and 0.0184 ± 0.0045, respectively. The highest (0.092) and the lowest (0.000) genetic distances were between Bali and Donggala cattle populations and among Galekan (kept in BCRS), Rambon, and POBA cattle populations, respectively. Both mtDNA network and phylogenetic analyses revealed two major maternal lineages (A and B) of the studied population. Most of the sampled individuals (69.33%, present in haplotype H8-H19) were linked to lineage B, which belonged to the same cluster with Bos javanicus. Overall, most of the Indonesian native and local cattle populations had a considerable genetic diversity and shared a common maternal origin with Bos javanicus.


Indonesian Cattle, Cytochrome b, Genetic Diversity, Phylogenetic Analysis

Full Text:



Agung P, Saputra F, Zein MSA, Wulandari AS, Putra WPB, Said S, Jakaria J. 2019. Genetic diversity of Indonesian cattle breeds based on microsatellite markers. Asian-Australas J Anim Sci. 32: 467-476.

Andalib S, Divani AA, Michel TM, Høilund-Carlsen PF, Vafaee MS, Gjedde A. 2017. Pandora's Box: mitochondrial defects in ischaemic heart disease and stroke. Expert Rev Mol Med. 19:e5.

Bandelt HJ, Forster P, Rohl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 16: 37-48.

Çiftci Y, Eroğlu O, Firidin Ş. 2013. Mitochondrial cytochrome b sequence variation in three Sturgeon species (A. stellatus Pallas, 1771, A. gueldenstaedtii Brandt, 1833, H. huso Linnaeus, 1758) from the Black Sea Coasts of Turkey. Turk J Fish Aquat Sci. 13: 291-303.

Decker JE, Mckay SD, Rolf MM, Kim J, Molina AA, Sonstegard TS, et al. 2014. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genetics. 10: e1004254.

Directorate of Livestock Breeding and Production. Jenis Rumpun Sapi. [cited 2020 April 6]. Available from:

Gao Y, Gautier M, Ding X, Zhang H, Wang Y, Wang X, Faruque MDO, Li J, Ye S, Gou X, Han J, Lenstra JA, Zhang Y. 2017. Species composition and environmental adaptation of indigenous Chinese cattle. Sci Rep. 7: 16196.

Hall T. 1999. Bioedit: a biological sequence alignment editor and analysis program for windows 95/98/nt. Nucleic Acids Symp Ser. 41: 95–98.

Harrison RG. 1989. Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends Ecol Evol. 4: 6-11.

Hartatik T, Putra WBP, Volkandari SD, Sumadi. 2015. Polymorphism of mtDNA cytochrome b gene of local cattle in Indonesia. J-SustaiN. 3: 21-24

Hartatik T, Maharani D, Sidadolog JHP, Fathoni A, Sumadi. 2018. Haplotype diversity of partial cytochrome b gene in Kebumen Ongole Grade cattle. Trop Anim Sci J. 41: 8-14.

Hartatik T, Hariyono DNH, Adinata Y. 2019. Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences. Biodiversitas 20: 17-22.

Jia S, Zhou Y, Lei C, Yao R, Zhang Z, Fang X, Chen H. 2010. A new insight into cattle's maternal origin in six Asian countries. J Genet Genomics. 37: 173-80.

Jakaria J, Musyaddad T, Rahayu S, Muladno M, Sumantri C. 2019. Diversity of D-loop mitochondrial DNA (mtDNA) sequence in Bali and Sumba Ongole cattle breeds. J Indonesian Trop Anim Agric. 44: 335-345.

Kikkawa Y, Takada T, Sutopo, Nomura K, Namikawa T, Yonekawa H, Amano T. 2003. Phylogenies using mtDNA and SRY provide evidence for male-mediated introgression in Asian domestic cattle. Anim. Genet. 34: 96–101.

Kim JH, Byun MJ, Kim MJ, Suh SW, Ko YG, Lee CW, Jung KS, Kim ES, Yu DJ, Kim WH, Choi SB. 2013. mtDNA diversity and phylogenetic state of Korean cattle breed, Chikso. Asian-Australas J Anim Sci. 26: 163-170.

Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular evolutionary genetic analysis version 7.0 for bigger datasets. Mol Biol Evol. 33: 1870-1874.

Li H, Slone J, Fei L, Huang T. 2019. Mitochondrial DNA variants and common diseases: a mathematical model for the diversity of age-related mtDNA mutations. Cells 8: 608.

Margawati ET, Volkandari SD, Indriawati, Ridwan M. 2018. Genetic diversity and relationship among Bali cattle from several locations in Indonesia based on ETH10 microsatellite marker. JITV. 23:168-173.

Mohamad K, Olsson M, Andersson G, Purwantara B, van Tol HTA, Rodriguez-Martinez H, Colenbrander B, Lenstra JA. 2011. The origin of Indonesian cattle and conservation genetics of the Bali cattle breed. Reprod Dom Anim 47: 18–20..

Othman OE, Abdel-Kader HAM, Alam SS, Abdel-Aziem SH. 2017. Cytochrome b conservation between six camel breeds reared in Egypt. J Genet Eng Biotechnol. 15: 1-6.

Pamungkas D, Antari R, Mayberry DE, Poppi DP. 2012. A growth comparison of Ongole and European Cross cattle kept by smallholder farmers in Indonesia. Proceeding of the 15th Asian-Australasian Association of Animal Production (AAAP) Animal Science Congress, Bangkok, Thailand.

Rahmatullaili S, Fatmawati D, Nisa C, Winaya A, Chamisijatin L, Hindun I. 2019. Genetic diversity of Bali cattle: cytochrome b sequence variation. IOP Conf Ser: Earth Environ Sci. 276: 012048.

Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol. 34: 3299-3302.

Sari EM, Jianlin H, Noor RR, Sumantri C, Margawati ET. 2016. Phylogenetic analysis of Aceh cattle breed of Indonesia through mitochondrial D-loop region. J Genet Eng Biotechnol. 14: 227-231.

Sharma R, Kishore A, Mukesh M, Ahlawat S, Maitra A, Pandey AK, Tantia MS. 2015. Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers. BMC Genet. 30: 16:73.

Sutarno, Setyawan AD, Lymbery AJ. 2015. Genetic diversity of five Indonesian native cattle breeds at microsatellite loci. Asian J Anim Sci. 9: 57-64.

Sutarno, Setyawan AD. 2016. Review: The diversity of local cattle in Indonesia and the efforts to develop superior indigenous cattle breeds. Biodiversitas. 17: 273–295.

Tarekegn GM, Ji X, Bai X, Liu B, Zhang W, Birungi J, Djikeng A,Tesfaye K. 2018. Variations in mitochondrial cytochrome b region among Ethiopian indigenous cattle populations assert Bos taurus maternal origin and historical dynamics. Asian-Australas J Anim Sci. 31: 1393-1400.

Thompson JD, Higgins DG, Gibson TJ. 1994. Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673–4680.

Winaya A, Muladno, Saefuddin A. 2015. Genetic diversity of Indonesian native cattle based on Y-chromosome microsatellite and its like-ladder DNA confirmation. J Anim Vet Adv. 14: 300-307.

Wolf C, Rentsch J, Hubner P. 1999. PCR-RFLP Analysis of Mitochondrial DNA: A reliable method for species identification. J Agric Food Chem. 47: 1350-1355.

Xia X, Qu K, Zhang G, Jia Y, Ma Z, Zhao X, Huang Y, Chen H, Huang B, Lei C. 2019. Comprehensive analysis of the mitochondrial DNA diversity in Chinese cattle. Anim Genet. 50: 70-73.

Yan L, She Y, Elzo MA, Zhang C, Fang X, Chen H. 2019. Exploring genetic diversity and phylogenic relationships of Chinese cattle using gene mtDNA 16S rRNA. Arch Anim Breed. 62: 325–333.


  • There are currently no refbacks.

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.