Haplotype Diversity of Partial Cytochrome b Gene in Kebumen Ongole Grade Cattle
Abstract
Cytochrome b gene is commonly used to figure out the genetic variation in animals. This research was designed to explore specific markers of Kebumen Ongole grade cattle and to understand the relationship between Kebumen and Brahman cattle using mtDNA cyt b sequences. The sequence of mtDNA cytochrome b gene of 14 individuals Kebumen Ongole grade cattle and 15 individuals Brahman cattle was determined by using polymerase chain reaction and sequencing with a pair of primer. The haploview software was utilized to linkage disequilibrium (LD) analysis. As a result, 36 SNPs (single nucleotide polymorphisms) with 8 haplotypes were identified in Kebumen Ongole grade cattle. In contrast, a small number of SNPs (7) and haplotypes (6) were observed in Brahman cattle. The homozigosity in Brahman cattle was higher than that in Kebumen Ongole grade cattle cattle. Moreover, based on mtDNA sequences, 50% of Kebumen Ongole grade cattle had 85% similarity with Brahman cattle. The SNP number and LD values of Kebumen Ongole grade cattle were greater than those of Brahman cattle. It was presumed that Brahman cattle might be introduced into Kebumen territory. In conclusion, some of Kebumen Ongole grade cattle have genetic relation with Brahman cattle. In addition, the information of SNP and haplotype results from this research can be used as markers to differentiate breeds of animals.
References
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Romaino, S. M. N. , Z. A. Fazly-Ann , S. S. Loo , M. M. Hafiz , M. D. Hafiz , M. I. Iswadi , P. Kashiani , M. K. A. Rosli , S. M. F. Syed-Shabthar , B. M. Md-Zain, & O. Abas-Mazni. 2014. Species identification of Malayan Gaur, Kedah-Kelantan and Bali cattle using polymerase chain reaction-restricted fragment length polymorphism. Genet. Mol. Res. 13: 406-414. https://doi.org/10.4238/2014.January.21.8
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Sudrajad, P. & Subiharta. 2014. Karakteristik fenotipik sapi betina Peranakan Ongole Kebumen. Widyariset. 17:283-290.
Septian, W. A., Jakaria, & C. Sumantri. 2015. Genetic diversity of Bali cattle based on microsatellite marker in Indonesian breeding centre. Med. Pet. 38:12-17. https://doi.org/10.5398/medpet.2015.38.1.12
Sutarno & A. D. Setyawan. 2015. Review: Genetic diversity of local and exotic cattle and their crossbreeding impact on the quality of Indonesian cattle. Biodiversitas:16:327-354.
Sutarno, A. D. Setyawan, & A. J. Lymbery. 2015. Genetic diversity of five Indonesian native cattle breeds at microsatellite loci. Asian J. Anim. Sci. 9:57-64. https://doi.org/10.3923/ajas.2015.57.64
Suyadi S, Hakim L, S. Wahjuningsih, & H. Nugroho. 2014. Reproductive performance of Peranakan Ongole (PO) and Limousin x PO Crossbreed (Limpo) cattle at different altitude areas in East Java, Indonesia. J Appl Sci Agric. 9: 81-85.
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Winaya, A., Muladno, R. E. Gunadi, & A. Saefuddin. 2009. Y chromosome microsatellite variation in Bali cattle (Bos sondaicus) population. Animal Production. 3:149-154.
Wolf, C., J. Rentsch, & P. Hubner. 1999. PCR-RFLP analysis of mitochondrial DNA: A Reliable Method for Species Identification. J. Agric. Food Chem. 47: 1350-1355. https://doi.org/10.1021/jf9808426
Yang, W. & R. J. Tempelman. 2012. A Bayesian antedependence model for whole genome prediction. Genetics 190: 1491–1501. https://doi.org/10.1534/genetics.111.131540
Zhou, L., X. Ding, Q. Zhang, Y. Wang, M. S. Lund, & G. Su. 2013. Consistency of linkage disequilibrium between Chinese and Nordic Holsteins and genomic prediction for Chinese Holsteins using a joint reference population. Genet. Sel. Evol. 45:1-7. https://doi.org/10.1186/1297-9686-45-7
Brito, F., J. Neto, M. Sargolzaei, J. Cobuci, & F. Schenkel. 2011. Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle. BMC Genet. 12 : 1-10. https://doi.org/10.1186/1471-2156-12-80
Cai, X., H. Chen, C. Lei, S. Wang, K. Xue, & Zhang, B. 2007. mtDNA diversity and genetic lineages of eighteen cattle breeds from Bos taurus and Bos indicus in China. Genetica. 131: 175-183. https://doi.org/10.1007/s10709-006-9129-y
Chen, S. Y., Y. P. Liu, & Y. G. Yao. 2010. Species authentication of commercial beef jerky based on PCR-RFLP analysis of the mitochondrial 12S rRNA gene. J. Genet. Genomics 37: 763-769. https://doi.org/10.1016/S1673-8527(09)60093-X
Chung, H. 2013. Phylogenetic analysis and characterization of mitochondrial DNA for Korean native cattle. Open Journal of Genetics. 3:12-23. https://doi.org/10.4236/ojgen.2013.31003
Cuyabano, B., G. Su, & M. Lund. 2014. Genomic prediction of genetic merit using LD-based haplotypes in the Nordic Holstein population. BMC Genom. 15(1171) : 1-11. https://doi.org/10.1186/1471-2164-15-1171
Espigolan, R., F. Baldi, A. A. Boligon, F. R. P. Souza, D. G. M. Gordo, R. L. Tonussi, D. F. Cardoso, H. N. Oliveira, H. Tonhati, M. Sargolzaei, F. S. Schenkel, R Carvalheiro, J. A. Ferro, & L. G. Albuquerque. 2013. Study of whole genome linkage disequilibrium in Nellore cattle. BMC Genom. 14: 1-8. https://doi.org/10.1186/1471-2164-14-305
Gurgul, A., E. Semik, K. Pawlina, T. Szmatoła, I. Jasielczuk, & M. Bugno-Poniewierska. 2014. The application of genome-wide SNP genotyping methods in studies on livestock genomes. J. Appl. Genet. 55:197–208. https://doi.org/10.1007/s13353-014-0202-4
Hartatik, T., T. S. M. Widi, S. D. Volkandari, D. Maharani, & Sumadi. 2014. Analysis of DNA Polymorphism in SRY Gene of Madura Cattle Populations. Procedia Environ. Sci. 20:365–369. https://doi.org/10.1016/j.proenv.2014.03.046
Hartatik, T., W. B. P. Putra., S. D. Volkandary, & Sumadi. 2015. Polymorphism of mtDNA Cytochrome b Gene of Local Cattle in Indonesia. J-SustaiN 3:1-24. https://doi.org/10.24910/jsustain/3.1/2124
Jasielczuk, I., A. Gurgul, T. Szmatoła, T. Ząbek, K. Pawlina, E. Semik, & M. Bugno Poniewierska. 2016. Linkage disequilibrium and haplotype block structure in Limousin, Simmental and native Polish Red cattle. Livestock Science. 191: 57–63. https://doi.org/10.1016/j.livsci.2016.07.008
Lee, S. H., Y. M. Cho, D. Lim, H. C. Kim, B. H. Choi, H. S. Park, O. H. Kim, S. Kim, T. H. Kim, D. Yoon, & S. K. Hong. 2011. Linkage Disequilibrium and Effective Population Size in Hanwoo Korean Cattle. Asian-Aust. J. Anim. Sci. 24: 1660 – 1665.
McKay, S. D., R. D. Schnabel, B. M. Murdoch, L. K. Matukumalli, J. Aerts, W. Coppieters, D. C. E. D. Neto, C. A. Gill, C. Gao, H. Mannen, P. Stothard, Z. Wang, C. P. V. Tassell, J. L. Williams, J. F. Taylor, & S. S. Moore. 2007. Whole genome linkage disequilibrium maps in cattle. BMC Genetics. 8:1-12. https://doi.org/10.1186/1471-2156-8-74
Miar, Y., M. Sargolzaei, & Flavio Schenkel. 2014. Haplotype phasing in dairy cattle. Dairy Cattle Breeding and Genetics Committee, Guelph.
Minarovič, T., A. Trakovická, A. Rafayová, & Z. Lieskovská. 2010. Animal Species Identification by PCR – RFLP of Cytochrome b. Animal Science and Biotechnologies. 43: 296 – 299.
Mokry, F. B., M. E. Buzanskas, M. A. Mudadu, D. A. Grossi, R. H. Higa, R. V. Ventura, A. O. Lima, M. Sargolzaei, S. L. C. Meirelles, F. S. Schenkel, M. V. Silva, S. C. M. Niciura, M. M. Alencar, D. P. Munari, & L. C Almeida Regitano. 2014. Linkage disequilibrium and haplotype block structure in composite beef cattle breed. BMC Genom. 15: 1-9. https://doi.org/10.1186/1471-2164-15-S7-S6
Munira, S., F. T. Jahura, Md. M. Hossain, & M. Shamsul 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. https://doi.org/10.3329/ajmbr.v2i2.29008
Niu, H., B. Zhu, P. Guo, W. Zhang, J. Xue, Y. Chen, L. Zhang, H. Gao, X. Gao, L. Xun, & J. Lin. 2016. Estimation of linkage disequilibrium levels and haplotype block structure in Chinese Simmental and Wagyu beef cattle using high-density genotypes. Livest. Sci. 190:1–9. https://doi.org/10.1016/j.livsci.2016.05.012
Qanbari, S., E. C. G. Pimentel, J. Tetens, G. Thaller, P. Lichtner, A. R. Sharifi, & H. Simianer. 2010. The pattern of linkage disequilibrium in German Holstein cattle. Anim. Genet. 41: 346–356.
Romaino, S. M. N. , Z. A. Fazly-Ann , S. S. Loo , M. M. Hafiz , M. D. Hafiz , M. I. Iswadi , P. Kashiani , M. K. A. Rosli , S. M. F. Syed-Shabthar , B. M. Md-Zain, & O. Abas-Mazni. 2014. Species identification of Malayan Gaur, Kedah-Kelantan and Bali cattle using polymerase chain reaction-restricted fragment length polymorphism. Genet. Mol. Res. 13: 406-414. https://doi.org/10.4238/2014.January.21.8
Stock, F., C. J. Edwards, R. Bollongino, E. K. Finlay, J. Burger, & D. G. Bradley. 2009. Cytochrome b sequences of ancient cattle and wild ox support phylogenetic complexity in the ancient and modern bovine populations. Anim. Genet. 40:694-700. https://doi.org/10.1111/j.1365-2052.2009.01905.x
Sudrajad, P. & Subiharta. 2014. Karakteristik fenotipik sapi betina Peranakan Ongole Kebumen. Widyariset. 17:283-290.
Septian, W. A., Jakaria, & C. Sumantri. 2015. Genetic diversity of Bali cattle based on microsatellite marker in Indonesian breeding centre. Med. Pet. 38:12-17. https://doi.org/10.5398/medpet.2015.38.1.12
Sutarno & A. D. Setyawan. 2015. Review: Genetic diversity of local and exotic cattle and their crossbreeding impact on the quality of Indonesian cattle. Biodiversitas:16:327-354.
Sutarno, A. D. Setyawan, & A. J. Lymbery. 2015. Genetic diversity of five Indonesian native cattle breeds at microsatellite loci. Asian J. Anim. Sci. 9:57-64. https://doi.org/10.3923/ajas.2015.57.64
Suyadi S, Hakim L, S. Wahjuningsih, & H. Nugroho. 2014. Reproductive performance of Peranakan Ongole (PO) and Limousin x PO Crossbreed (Limpo) cattle at different altitude areas in East Java, Indonesia. J Appl Sci Agric. 9: 81-85.
Utomo, B., R. Oelviani & Subiharta. 2015. Peningkatan performans pedet sapi Peranakan Ongole pasca sapih melalui perbaikan manajemen dengan pemanfaatan sumber daya lokal. Proceeding Seminar Nasional Masyarakat Biodiversitas Indonesia, 1: 838-842.
Winaya, A., Muladno, R. E. Gunadi, & A. Saefuddin. 2009. Y chromosome microsatellite variation in Bali cattle (Bos sondaicus) population. Animal Production. 3:149-154.
Wolf, C., J. Rentsch, & P. Hubner. 1999. PCR-RFLP analysis of mitochondrial DNA: A Reliable Method for Species Identification. J. Agric. Food Chem. 47: 1350-1355. https://doi.org/10.1021/jf9808426
Yang, W. & R. J. Tempelman. 2012. A Bayesian antedependence model for whole genome prediction. Genetics 190: 1491–1501. https://doi.org/10.1534/genetics.111.131540
Zhou, L., X. Ding, Q. Zhang, Y. Wang, M. S. Lund, & G. Su. 2013. Consistency of linkage disequilibrium between Chinese and Nordic Holsteins and genomic prediction for Chinese Holsteins using a joint reference population. Genet. Sel. Evol. 45:1-7. https://doi.org/10.1186/1297-9686-45-7
Authors
HartatikT., MaharaniD., SidadologJ. H. P., FathoniA., & SumadiS. (2018). Haplotype Diversity of Partial Cytochrome b Gene in Kebumen Ongole Grade Cattle. Tropical Animal Science Journal, 41(1), 8-14. https://doi.org/10.5398/tasj.2018.41.1.8
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