The origin of pesisir cattle based on D-loop mitochondrial DNA
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Abstract. Putri AE, Farajallah A, Perwitasari D. 2019. The origin of pesisir cattle based on D-loop mitochondrial DNA. Biodiversitas 20: 2569-2575. Pesisir cattle is one of Indonesia's local cattle descended from Bos indicus which has small body characteristics. It was assumed due to crossbreeding between pesisir cattle and other cattle. Therefore this study aims to study the origin of pesisir cattle based on the D-loop mtDNA region and to find out the phylogenetic relationships between pesisir cattle and other cattle. Cattle blood samples were taken in two locations, Krui Way and Tanah Rekah. Amplification of the mitochondrial gene using the primary pair of collections of Dr. Achmad Farajallah, namely AF22 (forward) 5'-GCGTACGCAATCTTACGATCA-3' and AF23 (reverse) 5'-ATGCAGTTAAGTCCAGCTAC-3'. Reconstruction of phylogenetic trees was analyzed using the Neighbor-Joining Method based on Kimura 2 Parameters. The results of the mtDNA analysis in the D-loop region showed that there were two broods in pesisir cattle, namely Bos indicus and Bos javanicus. The closeness between these species is due to the close geographical distance between Bos indicus originating from Way Krui, Lampung and Bos javanicus from Java.
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References
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Saladin R. 1983. Penampilan sifat-sifat produksi dan reproduksi sapi lokal Pesisir Selatan di Propinsi Sumatera Barat. Disertasi. Sekolah Pascasarjana, Institut Pertanian Bogor, Bogor.
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Tegelstrom H. 1986. Mitochondrial DNA in natural population: an improved routine for screening of genetic variation based on sensitive silver staining. Electrophoresis 7: 226-229.
Tripathi AK, Koringa PG, Jakhesara SJ, Ahir VB, Ramani UV, Bhatt VD, Sajnani MR, Patel DA, Joshi AJ, Shanmuga SJ, Rank DN, Joshi CG. 2011. A Preliminary sketch of horn cancer transcriptome in indian zebu catt;e. Gene 0378-1119.
Troy CS, MacHugh DE, Bailey JF, Magee DA, Loftus RT, Cunningham P, Chamberlain AT, Sykesk BC, & Bradley DG. 2001. Genetic Evidence For Near-Eastern Origins Of European Cattle. Nature. Vol 410.
Uggla CM. 2008. Investigating genetic variability within specific indigenous Indonesia cattle breed [Disertasi]. Swedish University of Agricultural Science.
Wang MS, Zeng Y, Wang X, Nie WH, Wang JH, Su WT, Otecko NO, Xiong ZJ, Wang S, Qu KX, Yan SQ, Yang MM, Wang W, Dong Y, Wu DD, and Zhang YP. 2017. Draft genome of the gayal, Bos frontalis, GigaScience, Volume 6, Issue 11, Hal 1-31.
Adrial. 2010. Potensi Sapi Pesisir dan Upaya Pengembangannya Di Sumatera Barat. Jurnal Litbang Pertanian: 29 (2).
Avise JC. 1994. Molecular Markers, Natural Hystory and Evolution. Chapman and Hall. New York.
Bradley DG, Machugh DE, Cunningham P, Loftus RT. 1996. Mitochondrial diversity and the origins of African and European cattle. Proc. Natl. Acad. Sci. USA 93: 5131-5135.
Duryadi D. 1994. Peran DNA mitokondria (mtDNA) dalam studi keragaman genetik dan biologi populasi pada hewan. J. Hayati 1(1) : 1-4.
Edwards CJ, Magee DA, Park SD, McGettigan PA, Lohan AJ, Murphy A, Finlay EK, Shapiro B, Chamberlain AT, Richards MB, Bradley DG, Loftus BJ, MacHugh DE. 2010. A Complete Mitochondrial Genome Sequence from a Mesolithic Wild Aurochs (Bos primigenius). Plos One. Vol 5 Issue 2, Hal 1-13.
Farajallah A. 2005. Kajian pembentukan ruas berulang dalam daerah pengontrol genom mitokondria labi-labi [Laporan Penelitian]. Bogor: Lembaga Penelitian dan Pemberdayaan Masyarakat, Institut Pertanian Bogor.
Firdhausi NF. 2010. Asal Usul Sapi Madura Berdasarkan Penanda Dna Mitokondria. [Thesis]. Bogor: Program Pascasarjana, Institut Pertanian Bogor.
Gemmel NJ, Western PS, Watson JM, Graves JAM. 1996. Evolution of the mammalian mitochondrial control region comparisons of control region sequences between monotreme and therian mammals. Mol Biol Evol. 13: 798808.
Hartatik T, Putra WBP, Volkandari SD, Sumadi. 2015. Polymorphism of mtDNA cytochrome b gene of local cattle in Indonesia. IJSFHS. 3(1): 22-24.
Hassanin A, Ropiquet A. 2007. Resolving a zoological mystery: the kouprey is a real species. Proc. R. Soc. 274: 2849-2855.
Hassanin A, Delsuc F, Ropiquet A, Hammer C, Vuuren BJV, Matthee C, Garcia MR, Catzeflis F, Areskoung V, Nguyen TT, Couloux A. 2012. Pattern and timing of diversification of Certartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. Compets Rendus Biologies. 1631-0691.
Hiendleder S, Kaupe B, Wassmuth R, Janke A. 2002. Molecular analysis of wild and domestic sheep questions current nomenclature and provides evidence for domestication from two different subspecies. Proc R Soc Lond 269: 893–904.
Mannen H, Tsuji S, Loftus RT, Bradley DG. 1998. Mitochondrial DNA variation and evolution of Japanese black cattle (Bos taurus). Genetics 150: 1169-1175.
Martojo H. 2003. Indigenous Bali Cattle: The Best Suited Cattle Breed for Sustainable Small Farms in Indonesia. Laboratory of Animal Breeding and Genetics, Fac. Anim. Sci., Bogor Agric. Univ., Indonesia.
Matsubayashi H, Hanzawa K, Kono T, Ishige T, Gakuhari T , Lagan P, Sunjoto I, Sukor JRA, Sinun W, dan Ahmad AH. 2014. First molecular data on Bornean banteng Bos javanicus lowi (Cetartiodactyla, Bovidae) from Sabah, Malaysian Borneo. Mammalia. Vol 78 Issue 4, Hal 1-9.
Mohammad K, Olsson M, Tol HTAV, Mikko S, VlamingsbBH, Andersson G, Matinez HR, Purwantara B, Paling RW, Colenbrander B, Lenstra JA. 2009. On the Origin of Indonesian Cattle. Plos One. Vol 4, Issue 5, Hal 1-6.
Na RS, Zhao YJ, Gao HJ, An TW, Huang YF, E GX. 2014. Complete mitochondrial genome of the Yakow (Bos primigenius taurus x Bos grunniens) in China. Mitochondrial DNA. 27 (6) : 3826-3827.
Namikawa TY, Matsuda K, Kondo B, Pangestu, Martojo. 1982. Blood groups and blood protein polymorphisms of different types of cattle in Indonesia. Ditto 35-46.
Martinez-Navarro B, Karoui-Yakoub N, Oms O, Amri L, Lopez-Garcia JM, Zerai K, Hugues-Alexandre B, Moncef-Said M, Maria-Patrocinio E, Ali NBH et al. 2014. The early middle pleistocene archeopaleontological site of Wadi Sarrat (Tunisia) and the earliest record of Bos primigenius. Quaternary Sciences 90: 37-46
Nei M, Kumar S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York.
Nijman IJ, Otsen M, Verkaar ELC, Ruitjer CD, Hanekamp E, Ochieng JW, Shamshad S, Rege JEO, Hannotte O, Barwegen MW, Sulawati T, Lenstra JA. 2003. Hybridization of banteng (Bos javanicus) and zebu (Bos indicus) revealed by mitochondrial DNA, satellite DNA, AFLP microsatelites. Heredity 90:10-16.
Pessole G, Gissi C, Chirico AD, Saccone C. 1999. Nucleotide subtitution rate of mammalian mitochondrial genomes. J Mol Evol 48:427-434.
Pénzes ZS., Csanádi GY, Kovács MG, Beer ZS. 2002. Molecular markers in ecology. Tiscia 33: 9-30.
Saladin R. 1983. Penampilan sifat-sifat produksi dan reproduksi sapi lokal Pesisir Selatan di Propinsi Sumatera Barat. Disertasi. Sekolah Pascasarjana, Institut Pertanian Bogor, Bogor.
Sarbaini. 2004. Kajian Keragaman Karakteristik Eksternal DNA Mikrosatelit Sapi Pesisir Sumatera Barat. Disertasi. Sekolah Pascasarjana IPB. Bogor.
Tamura K, Stecher G, Peterson D, Filipski A, and Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol. Biol. Evol. 30(12):2725–2729
Tegelstrom H. 1986. Mitochondrial DNA in natural population: an improved routine for screening of genetic variation based on sensitive silver staining. Electrophoresis 7: 226-229.
Tripathi AK, Koringa PG, Jakhesara SJ, Ahir VB, Ramani UV, Bhatt VD, Sajnani MR, Patel DA, Joshi AJ, Shanmuga SJ, Rank DN, Joshi CG. 2011. A Preliminary sketch of horn cancer transcriptome in indian zebu catt;e. Gene 0378-1119.
Troy CS, MacHugh DE, Bailey JF, Magee DA, Loftus RT, Cunningham P, Chamberlain AT, Sykesk BC, & Bradley DG. 2001. Genetic Evidence For Near-Eastern Origins Of European Cattle. Nature. Vol 410.
Uggla CM. 2008. Investigating genetic variability within specific indigenous Indonesia cattle breed [Disertasi]. Swedish University of Agricultural Science.
Wang MS, Zeng Y, Wang X, Nie WH, Wang JH, Su WT, Otecko NO, Xiong ZJ, Wang S, Qu KX, Yan SQ, Yang MM, Wang W, Dong Y, Wu DD, and Zhang YP. 2017. Draft genome of the gayal, Bos frontalis, GigaScience, Volume 6, Issue 11, Hal 1-31.
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