Cece SUMANTRI, Jakaria JAKARIA, Restu MISRIANTI, Sony Hartono WIJAYA

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

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 (π) 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.

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1. Sutarno S, Setyawan AD. Review: The diversity of local cattle in Indonesia and the efforts to develop superior indigenous cattle breeds. Biodiversitas Journal of Biological Diversity 2016; 17: 273-295. doi: 10.13057/biodiv/d170139
2. Hartatik T, Putra WBP, Volkandari SD, Sumadi S. Polymorphism of mtDNA cytochrome b gene of local cattle in Indonesia. International Journal of Sustainable Future for Human Security 2015; 3: 21-24. doi: 10.24910/jsustain/3.1/2124
3. Xia X, Qu KX, Zhang G, Lei C. Comprehensive analysis of the mithocondrial DNA Diversity in Chinase Cattle. Animal Genetics 2018; 50: 1-4. doi: 10.1111/age.12749
4. Tarekegn GM, Ji XY, Bai X, Liu B, Zhang W et al. Variations in mithocondrial cytochrome b region among Ethiophian indigineous cattle populations assert Bos taurus maternal origin and historical dynamics. Asian-Australasian Journal of Animal Sciences 2018; 31: 1393-1400. doi: 10.5713/ajas.17.0596
5. Jakaria J, Musyaddad T, Rahayu S, Muladno M, Sumantri C. Diversity of D-loop mitochondrial DNA (mtDNA) sequence in Bali and Sumba Ongole cattle breeds. Journal of the Indonesian Tropical Animal Agriculture 2019; 44: 335-345. doi: 10.14710/ jitaa.44.4.335-345
6. Sari EM, Jianlin H, Noor RR, Sumantri C, Margawati ET. Phylogenetic analysis of Aceh cattle breed of Indonesia through mitochondrial D-Loop region. Journal, Genetic Engineering and Biotechnology 2016; 14: 227-231. doi: 10.1016/j.jgeb.2015.12.001
7. Hartatik T, Maharani D, Sidadolog JHP, Fathoni A, Sumadi S. Haplotype diversity of partial cytochrome b gene in Kebumen Ongole grade cattle. Tropical Animal Science Journal 2018; 41: 8-14. doi: 10.5398/tasj.2018.41.1.8
8. Hartatik T, Hariyono DNH, Adinata Y. Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences. Biodiversitas Journal of Biological Diversity 2019; 20: 17-22. doi: 10.13057/biodiv/d200103
9. Prihandini PW, Primasari A, Luthfi M, Efendy J, Pamungkas D. Genetic diversity of mitochondrial dna cytochrome b in Indonesian native and local cattle populations. Jurnal Ilmu Ternak Dan Veteriner 2020; 25: 39-47. doi: 10.14334/jitv.v25i2.2496
10. Yan L, She Y, Elzo MA, Zhang C, Fang X, Chen H. Exploring genetic diversity and phylogenic relationships of Chinese cattle using gene mtDNA 16S rRNA. Archives Animal Breeding 2019; 62: 325-333. doi: 10.5194/aab-62-325-2019
11. Mahmoodi M, Afshari K, Seyedabadi AH, Mehran. Sequence analysis of 12S rRNA and 16S rRNA mitochondrial genes in Iranian Afshari sheep. Banat’s Journal of Biotechnology 2018; 18: 5-11. doi: 10.7904/2068–4738–IX(18)–5
12. Lin Q, Li MW, Wang YZ, Qiu HJ. Determination and phylogenetic analysis of the complete mitochondrial genome of Bubalus bubalis Linnaeus, 1758 breed Nili-Ravi (Artiodactyla: Bovidae). Mitochondrial DNA. Part B, Resources 2020; 5: 461- 462. doi: 10.1080/23802359.2019.1704182
13. Seyedabadi HR, Savar SS, Eydivandi C, Harasi I. Genetic and phylogenetic analysis of the mitochondrial genome in Khuzestan buffalo. Agricultural Biotechnology Journal 2019; 11: 175-190. doi: 10.22103/JAB.2019.2480
14. Kuznetsova MV, Kholodova MV, Luschekina AA. Phylogenetic analysis of Sequencesof the 12S and 16S rRNA mitochondrial Genesin the family Bovidae: New evidence. Russian Journal of Genetics 2002; 38: 942-950. doi: 10.1023/A:1016891913078
15. Arif IA, Bakir MA, Khan HA. Inferring the phylogeny of Bovidae using mitochondrial DNA sequences: Resolving power of individual genes relative to complete genomes. Evolutionary Bioinformatics Online 2012; 8: 139-150. doi: 10.4137/EBO.S8897
16. Kumar S, Stecher G, Li M, Knyaz C, Tamura K, Mega X. Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution 2018; 35: 1547- 1549. doi: 10.1093/molbev/msz312
17. Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P et al. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Molecular Biology and Evolution 2017; 34: 3299-3302. doi: 10.1093/molbev/msx248
18. Bandelt HJ, Forster P, Röhl A. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 1999; 16: 37-48
19. Leigh JW, Bryant D. PopART: Full-feature software for haplotype network construction. Methods in Ecology and Evolution 2015; 6: 1110-1116. doi: 10.1111/2041-210X.12410
20. Susari NNW, Suastika IP, Agustina KK. Molecular analysis of Taro and Bali cattle using cytochrome oxidase subunit I (COI) in Indonesia. Biodiversitas Journal of Biological Diversity 2021; 22: 165-172. doi: 10.13057/biodiv/d220122
21. Mohamad K, Olsson M, Andersson G, Purwantara B, Tol HV et al. The origin of Indonesian cattle and conservation genetics of the Bali cattle breed. Reproduction in Domestic Animals 2011; 2011(47 (1)) Supplement 1: 1-4. doi: 10.1111/j.1439- 0531. 2011.01960.x
22. Jakaria J, Alwiyah N, Saputra F, Baihaqi M, Noor RR. Genetic diversity between Bali cattle (Bos javanicus) and it’s hybrids using microsatellite markers. Iranian Journal of Applied Animal Science 2020; 10: 453-460
23. Firdhausi NF, Farajallah A, Perwitasari D. Phylogenetic study of madura cattle based on mitochondrial cyt b and D-loop sequences. Buletin Peternakan 2021; 45: 14-20. doi: 10.21059/ buletinpeternak.v45i1.48557
24. Wulandari A, Nurgiartiningsih VMA, Kuswati STE, Partogi PA. Kinship of several Indonesian local cattle by using DNA mitochondrial COI (cytochrome oxidase Sub-unit I). International Research Journal of Advanced Engineering and Science 2019; 4: 165-167. doi: 10.5281/zenodo.3360536
25. Agung PP, Saputra F, Zein MSA, Wulandari AS, Putra WPB et al. Genetic diversity of Indonesian cattle breeds based on microsatellite markers. Asian-Australasian Journal of Animal Sciences 2019; 32: 467-476. doi: 10.5713/ajas.18.0283