Identification of a Differentiation Factor of Indonesian Ongole Cattle Breeds Based on Microsatellite Markers and Mitochondrial DNA

https://doi.org/10.21059/buletinpeternak.v42i3.33724

Paskah Partogi Agung(1*), Alfandy Hermansyah(2)

(1) Research Center for Biotechnology-Indonesian Insitute of Sciences, Cibinong, 16911, Indonesia
(2) Graduate School of Surya University
(*) Corresponding Author

Abstract


This study was conducted to identify the differentiation factor of Indonesian Ongole cattle breeds (Sumba Ongole and Ongole Grade) based on the 12 microsatellite markers and Cyt b gene polymorphism. A total of 50 blood samples (25 samples for each cattle breed) were used in this study. The multiplex DNA fragment analysis was conducted for allele identification based on the microsatellite markers. The haplotype identification (based on the mitochondrial DNA) was conducted using restriction fragment length polymorphism (RFLP) analysis with three restriction enzymes i.e. HinfI, HaeIII, and XbaI. Twelve microsatellite loci in this study revealed high polymorphism. A total of 82 alleles were detected in the SO cattle and 117 alleles were detected in the PO cattle. The TGLA227 and ETH225 were specific locus candidates which are different in the size and the number of alleles in the SO and PO cattle breeds. The B (HinfI), D (HaeIII), and Y (XbaI) haplotypes were found only in the PO cattle breed samples. The X haplotype was found in all samples of the SO cattle breed but was not found in all samples of the PO cattle breed. The Y haplotype was found in all samples of the PO cattle breed but was not found in all samples of the SO cattle breed. It can be concluded that the TGLA227 and ETH225 (based on microsatellite markers) and the B, D, X, and Y haplotypes (based on the mitochondrial DNA) can be considered as the differentiation factors between the SO and PO cattle breeds.

Keywords


Differentiation; Identification; Microsatellite; Mitochondria; Ongole

Full Text:

PDF


References

Agung, P. P., S. Anwar, A. S. Wulandari, A. Sudiro, S. Said, and B. Tappa. 2015. The potency of Sumba Ongole (SO) cattle: a study of genetic characterization and carcass productivity. J. Indonesian Trop. Anim. Agric. 40: 1-78.

Agung, P. P., F. Saputra, W. A. Septian, Lusiana, M.S. A. Zein, S. Sulandari, S. Anwar, A. S.Wulandari, S. Said, and B. Tappa. 2016.Study of genetic diversity amongSimmental cross cattle in West Sumatrabased on microsatellite markers. Asian-Australas. J. Anim. Sci. 29: 176-183.

Cervini, M., F. Henrique-Silva, N. Mortari, and E. Matheucci Jr. 2006. Genetic variability of 10 microsatellite markers in the characterization of Brazilian Nellore cattle (Bos indicus). Genet. Mol. Biol. 29: 486-490.

Czerneková, V., T. Kott, G. Dudková, Z. Sztankóová, and J. Soldát. 2006. Genetic diversity between seven Central European cattle breeds as revealed by microsatellite analysis Czech J. Anim. Sci. 51: 1-7.

Farag, M. R., T. S. Imam, and K. Dhama. 2015. Identification of some domestic animal species (camel, buffalo and sheep) by pcr-rflp analysis of the mitochondrial cytochrome b gene. Adv. Anim. Vet. Sci. 3: 136-142.

Glaubitz, J. C. 2004. Convert: a user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol. Ecol. Notes. 4: 309-310.

Gustafsson, C. M., M. Falkenberg, and N-G. Larsson. 2016. Maintenance and expression of mammalian mitochondrial DNA. Annu. Rev. Biochem. 85: 9.1–9.28.

Haasl, R. J. and B. A. Payseur. 2012. Microsatellites as targets of natural selection. Mol. Biol. Evol. 30: 285-298.

Hardjosubroto, W. 2004. Alternative policy in managing sustainable genetic resources of local beef cattle for national livestock breeding system. Wartazoa 14: 93-97.

Hartatik, T., W. B. P. Putra, S. D. Volkandari, and Sumadi. 2015. Polymorphism of mtDNA Cytochrome b Gene of Local Cattle in Indonesia. J-SustaiN 3: 21-24.

Kalinowski, S. T., M. L. Taper, and T. C. Marshall. 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol. Ecol. 16: 1099-1106.

Kesvulu, P. C., G. N. Rao, A. S. N. Ahmed, and B. R.Gupta. 2009. Molecular geneticcharacterization of Pungular cattle.Taminaldu J. Vet. Anim. Sci. 5: 179-185.

Ladoukakis, E. D. and E. Zouros. 2017. Evolution and inheritance of animal mitochondrial DNA: rules and exceptions. J. Biol. Res. (Thessalon). 24: 1-7.

Maretto, F., J. Ramljak, F. Sbarra, M. Penasa, R. Mantovani, and A. Ivankovic. 2012. Genetic relationships among Italian and Croatian Podolian cattle breeds assessed by microsatellite markers. Livest. Sci. 150: 256-264.

Ministry of Agriculture of the Republic of Indonesia. 2014. Ministerial Decree No. 427>Kpts>SR.120>3>2014 tentang penetapan rumpun sapi Sumba Ongole. http:>>bibit.ditjennak.pertanian.go.id>content>sapi-sumba-ongole. Accesed 23 August 2017.

Mohamad, K., M. Olsson, H. T. A. van Tol, S. Mikko, B. H. Vlaming, G. Andersson, H. Rodriguez-Martinez, B. Purwantara, R. W. Paling, B. Colenbrader, and J. A. Lenstra. 2009. On the origin of Indonesian cattle. PLoS ONE 4: e5490.

Munira, S., F. T. Jahura, Md. M. Hossain and M. S. A. Bhuiyan. 2016. Molecular detection of cattle and buffalo species meat origin using mitochondrial cytochrome b (Cyt b) gene. Asian J. Med. Biol. Res. 2: 177-182.

Nei, M. and S. Kumar. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York.

Riojas-Valdes, V. M., J. C. Gomes-de-la-Fuente, J. M. Garza-Lozano, D. C. Gallardo-Blanco, J. N. De Tellitu-Schutz, A. Wong-Gonzales, G. Davalos-Aranda, and J. A. Salinas-Melendez. 2009. Exclusion probabilities of 8 DNA microsatellites in 6 cattle breeds from Northeast Mexico. J. Anim. Vet. Adv. 8: 62-66.

Radko, A. 2010. Application of a complementary set of 10 microsatellite DNA markers for parentage verification in Polish Red cattle. Ann. Anim. Sci. 10: 9-15.

Rehman, M. S. and M. S. Khan. 2009. Genetic diversity of Hariana and Hissar cattle from Pakistan using microsatellite analysis. Pakistan Vet. J. 29: 67-71.

Rutledge, L. Y., C. J. Garroway, K. M. Loveless and B. R. Patterson. 2010. Genetic differentiation of eastern wolves in Algonquin Park despite bridging gene flow between coyotes and grey wolves. Heredity 105: 520-531.

Satish, A. Kumar, Y. Singh, Minakshi and G. Prasad. 2009. Cytochrome- b gene based PCR for identification and differentiation of cooked meat of sheep, goat, cattle, pig and poultry. Haryana Vet. 48: 53-57.

Seo, J. H., J. H. Lee, and H. S. Kong. 2017. Assessment of genetic diversity and phylogenetic relationships of Korean native chicken breeds using microsatellite markers. Asian-Australas. J. Anim. Sci. 30: 1365-1371.

Sharma, R., A. Kishore, M. Mukesh, S. Ahlawat, A. Maitra, A. K. Pandey, and M. S. Tantia. 2015. Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers. BMC Genetics 16: 1-12.

Stevanovic, J., Z. Stanimirovic, V. Dimitrijevic, and M. Maletic. 2010. Evaluation of 11 microsatellite loci for their use in paternity testing in Yugoslav Pied cattle (YU Simmental cattle). Czech J. Anim. Sci. 55: 221-226.

Stewart, J. B. and P. F. Chinnery. 2015. The dynamics of mitochondrial DNA heteroplasmy: implications for human health and disease. Nat. Rev. Genet.16: 530-542.

Sudrajad, P. and S. Subiharta. 2012. Karakter fenotipik sapi betina Peranakan Ongole (PO) kebumen. Widyariset 17: 283-290.

Suyadi, S., L. Hakim, S. Wahjuningsih, and H. Nugroho. 2014. Reproductive performance of Peranakan Ongole (PO)-and Limousin x PO Crossbred (Limpo) cattle at different altitude areas in East Java, Indonesia. J. Appl. Sci. Agric. 9: 81-85.

Yeh, F. C. and T. J. B. Boyle. 1997. Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belg. J. Bot. 129: 157-163.

Zarringhabaie, G. E., N. Pirany and A. Javanmard. 2011. Molecular multiplex PCR. Afri. J. Biotechnol. 10: 16461-16465.



DOI: https://doi.org/10.21059/buletinpeternak.v42i3.33724

Article Metrics

Abstract views : 10536 | views : 2148

Refbacks

  • There are currently no refbacks.


Bookmark and Share


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

Buletin Peternakan (Bulletin of Animal Science) Indexed by:

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