Phylogenetical Relationships between Kejobong Goat and Other Goats Based on Mt-DNA D-loop Sequence Analysis

D. A. Lestari, E. Purbowati, S. Sutopo, E. Kurnianto

Abstract


The aim of this study was to investigate phylogenetical relationships between Kejobong goat and Kacang goat as well as Etawah Grade goat using genetic diversity, haplotype, and genetic distance analysis based on D-loop sequences. A total of 76 blood samples belonged to three local goats, namely Kacang goat (KC), Etawah Grade goat (EG), and Kejobong goat (KJ). The DNA genome was extracted based on the manufacturer’s standard protocol using gSYNC DNA Mini Kit (Geneaid Biotech Ltd.) for sequence analysis control region (D-loop) in mitochondrial DNA (mtDNA) using specific primer. The results revealed that there were a total of 36 nucleotide substitutions, those were 1 indel (insertion or deletion), 34 haplotypes with Pi = 0.00253±0.00029 and Hd = 0.925±0.018 in three local goats, while intra-breed in this study showed Pi value of EG, KC, and KJ were 0.00452±0.00077, 0.00214±0.00028 and 0.00143±0.00018, respectively and Hd value were 0.985±0.025, 0.926±0.032, and 0.855±0.044, respectively. Genetic distances between KJ and KC, KJ and EG, and between KC and EG were 0.0018; 0.0034, and 0.0036, respectively. The highest NHap was observed in KC (17), followed by EG (15) and KJ (11); and all three local goats were in the same cluster in phylogeny tree. In conclusion, genetically, Kejobong goat is a crossbred of Kacang goat and Etawah Grade goat and has closer genetic relationships to Kacang goat than to Etawah Grade goat.

Keywords


genetic diversity; haplotype; genetic distance; d-loop; local goat

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Abdullah, M. A. N., H. Martojo, R. R. Noor, & D. D. Solihin. 2012. Genetic characterization of the Aceh Cattle using phenotypic, mitochondrial DNA of D-loop region and microsatellite DNA Analyses. Reprod. Dom. Anim. 47:15-17. https://doi.org/10.1111/j.1439-0531.2011.01959.x

Ahmed, S., P. Grobler, T. Madisha, & A. Kotze. 2017. Mitochondrial D-loop sequences reveal a mixture of endemism and immigration in Egyptian goat populations. Mitochondrial DNA A DNA Mapp. Seq. Anal. 28:711-716. https://doi.org/10.3109/24701394.2016.1174225

Akis, I., K. Oztabak, A. Mengi, & C. Un. 2014. Mitochondrial DNA diversity of Anatolian indigenous domestic goats. J. Anim. Breed. Genet. 131:487-495. https://doi.org/10.1111/jbg.12096

Al-Araimi, A., R. M. Al-Atiyat, O. M. Gaafar, R. Vasconcelos, A. L. Neira, M. O. Eisa, N. Amir, M. H. Benaissa, A. A. Alfaris, R. S. Aljumaah, S. M. Elnakhla, M. M. I. Salem, I. A. Ishag, M. E. Khasmi, & A. B. Pereira. 2017. Maternal genetic diversity and phylogeography of native Arabian goats. Livest. Sci. 206: 88-94. https://doi.org/10.1016/j.livsci.2017.09.017

Amills, M., O. Ramírez, A. Tomàs, B. Badaoui, J. Marmi, J. Acosta, A. Sànchez, & J. Capote. 2009. Mitochondrial DNA diversity and origins of South and Central American goats. Anim. Genet. 40:315-322. https://doi.org/10.1111/j.1365-2052.2008.01837.x

Awotunde, E.O., M. N. Bemji, O. Olowofeso, I. J. James, O. Ajayi, & A. O. Adebambo. 2015. Mitochondrial DNA sequence analyses and phylogenetic relationships among two Nigerian goat breeds and the South African Kalahari Red. Anim. Biotechnol. 26:180-187. https://doi.org/10.1080/10495398.2014.977907

Azor, P. J., L. V. Monteagudo, M. Luque, M. T. Tejedor, E. Rodero, I. Sierra, M. Herrera, A. Rodero, & M. V. Arruga. 2005. Phylogenetic relationships among Spanish goat breeds. Anim. Genet. 36:423-425. https://doi.org/10.1111/j.1365-2052.2005.01327.x

Batubara, A., R. R., Noor, A, Fajallah, B. Tiesnamurti, & M. Doloksaribu. 2011. Karakterisasi molekuler enam subpopulasi kambing lokal Indonesia berdasarkan analisis sekuen daerah D-loop DNA mitokondria. Indo. J. Anim. Vet. Sci.16: 49-60.

Benjelloun, B., F. Pompanon, M. B. Bati, M. Chentouf, M. Ibnelbachyr, B. E. Amiri, D. Rioux, B. Boulanouar, & P.

Taberlet. 2011. Mitochondrial DNA polymorphism in Moroccan goats. Small Rum. Res. 98:201-205. https://doi.org/10.1016/j.smallrumres.2011.03.041

Charlesworth, D., & J. H. Willis. 2009. The genetics of inbreeding depression. Genetics 10:783-796. https://doi.org/10.1038/nrg2664

Chen, S.Y., Y. H. Su, S. F. Wu, T. Sha & Y. P. Zhang. 2005. Mitochondrial diversity and phylogeographic structure of Chinese goats. Mol. Phylogenet. Evol. 37: 804-814. https://doi.org/10.1016/j.ympev.2005.06.014

Colli, L., H. Lancioni, I. Cardinali, A. Olivieri, M. R. Capodiferro, M. Pellecchia, M. Rzepus, W. Zamani, S. Naderi, & F. Gandini. 2015. Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability. BMC Genomic. 16:11-15. https://doi.org/10.1186/s12864-015-2342-2

Fan, B., S. L. Chen, J. H. Kijas, B. Liu, M. Yu, S. H. Zhao, M. J. Zhu, T. A. Xiong, & K. Li. 2007. Phylogenetic relationships among Chinese indigenous goat breeds inferred from mitochondrial control region sequence. Small Rumin. Res. 73: 262-266. https://doi.org/10.1016/j.smallrumres.2006.12.007

Febriana, A., S. Sutopo, & E. Kurnianto. 2017. Identification of BMP-15 Exon 2 for fecundity traits by PCR-RFLP and nucleotide sequence in Kejobong goat. J. Indo. Trop. Anim. Agric. 42:220-226. https://doi.org/10.14710/jitaa.42.4.220-226

Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x

Fernandez, H., S. Hughes, J. D. Vigne, D. Helmer, G. Hodgins, C. Miquel, C. Hanni, G. Luikart, & P. Taberlet. 2006. Divergent mtDNA lineages of goats in an Early Neolithic site, far from the initial domestication areas. Proc. Natl. Acad. Sci. 103:15375-15379. https://doi.org/10.1073/pnas.0602753103

Genbank. https://www.ncbi.nlm.nih.gov/genbank/ Accessed on January, 11st 2018.

Githui, E., F. Kibegwa, J. Kamau, S. Mutura, Z. Okwany, D. Ngigi, & E. Mwangi. 2016. Genetic relationships of indigenous goats reared by pastoralists in Kenya based on mitochondria D-loop sequence. Anim. Genet. Resour. 59:73-80. https://doi.org/10.1017/S2078633616000217

Groeneveld, L. F., J. A. Lenstra, H. Eding, M. A. Toro, B. Scherf, D. Pilling, R. Negrini, E. K. Finlay, H. Jianlin, E. Groeneveld, S. Weigend, & The Globaldiv Consortium. 2010. Genetic diversity in farm animals – a review. Anim. Genet. 41:6-31. https://doi.org/10.1111/j.1365-2052.2010.02038.x

Harlistyo, M. F., S. Sutopo, & E. Kurnianto. 2014. Genetic diversity of Kejobong goat based on mitochondrial DNA D-loop sequence. J. Indonesian Trop. Anim. Agric. 39:204-209. https://doi.org/10.14710/jitaa.39.4.204-209

Jia, Y. H., X. W. Shi, C. S. Jian, W. S. Zhu, Y. P. Zhang, Z. Q. He, Z. L. Liao, Y. H. Yu, & T. Q. Li. 1999. Mitochondrial DNA polymorphism of Guizhou goat breeds. Zoological Research 20: 88-92.

Jiyanto, S. Sutopo & E. Kurnianto. 2014. The genetic diversity of Kejobong goat based on Cytochrome B gene. J. Indo. Trop. Anim. Agric. 39:75-82. https://doi.org/10.14710/jitaa.39.2.75-82

Joshi, M. B., P. K. Rout, A. K. Mandal, C. Tyler-Smith, L. Singh, & K. Thangaraj. 2004. Phylogeography and origin of Indian domestic goats. Mol. Biol. Evol. 21: 454-462. https://doi.org/10.1093/molbev/msh038

Kibegwa, F., K. Githui, J. Jung’a, M. Badamana, & M. Nyamu. 2016. Mitochondrial DNA variation of indigenous goats in Narok and Isiolo counties of Kenya. J. Anim. Breed. Genet. 133:238–247. https://doi.org/10.1111/jbg.12182

Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120. https://doi.org/10.1007/BF01731581

Kurnianto, E., S. Sutopo, & E. Purbowati. 2012. Penampilan Fenotipik dan Genotipik Kambing Kejobong. Badan Penerbit Universitas Diponegoro, Semarang.

Kurnianto, E., S. Sutopo, E. Purbowati, E. T. Setiatin, D. Samsudewa, & T. Permatasari. 2013. Multivariate analysis of morphological traits of Local Goats in Central Java, Indonesia. Iranian J. Appl. Anim. Sci. 3: 361-367.

Lestari, D. A., Sutopo, & E. Kurnianto. 2017. Amino acid diversity on the basis of cytochrome b gene in Kacang and Ettawa Grade goats. J. Indo. Trop. Anim. Agric. 42:135-146. https://doi.org/10.14710/jitaa.42.3.135-146

Librado, P. & J. Rozas. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452. https://doi.org/10.1093/bioinformatics/btp187

Lin, B. Z., S. Odahara, M. Ishida, T. Kato, S. Sasazaki, & H. Mannen. 2013. Molecular phylogeography and genetic diversity of East Asian goats. Anim. Genet. 44:79-85. https://doi.org/10.1111/j.1365-2052.2012.02358.x

Liu, J. B., F. Wang, X. Lang, X. Zha, X. P. Sun, Y. J. Yue, R. L. Feng, B. H. Yang & J. Guo. 2013. Analysis of geographic and pairwise distance among Chinese Cashmere goat populations. Asian-Aust. J. Anim. Sci. 26:323-333. https://doi.org/10.5713/ajas.2012.12500

Liu, R. Y., L. Chu-Zhao, & Y. Gong-She. 2007. Genetic diversity and origin of Chinese domestic goats revealed by complete mtDNA D-loop sequence variation. Asian Australas. J. Anim. Sci. 20:178-183. https://doi.org/10.5713/ajas.2007.178

Liu, R. Y., Y. Gong-She, & L. Chu-Zhao. 2006. The genetic diversity of mtDNA D-loop and origin of Chinese goats. Acta Genetica Sinica. 33:420-428. https://doi.org/10.1016/S0379-4172(06)60069-3

Luikart, G., L. Gielly, L. Excoffier, J. D. Vigne, J. Bouvet & P. Taberlet. 2001. Multiple maternal origins and weak phylogeographic structure in domestic goats. Proc. Natl. Acad. Sci. U.S.A. 98:5927-5932. https://doi.org/10.1073/pnas.091591198

Mannen, H., Y. Nagata, & S. Tsuji. 2001. Mitochondrial DNA reveal that domestic goat (Capra hircus) are genetically affected by two subspecies of Bezoar (Capra aegagrus). Biochem. Genet. 39:145-154. https://doi.org/10.1023/A:1010266207735

Mason, I. L. 1984. Evolution of Domesticated Animals. Prentice Hall Press, New York, USA. P. 468.

Ministry of Agriculture. 2012. Decree on Rumpun Kacang Goat 2840/Kpts/LB.430/8/2012.

Ministry of Agriculture. 2013. Decree on Rumpun Etawah Grade Goat 695/Kpts/PD.410/2/2013.

Ministry of Agriculture. 2017. Decree on Rumpun Kejobong Goat 301/Kpts/SR.120/5/2017.

Naderi, S., H. R. Rezaei, F. Pompanon, M. G. B. Blum & R. Negrini. 2008. The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals. Proc. Natl. Acad. Sci. USA 105:17659-17664. https://doi.org/10.1073/pnas.0804782105

Naderi, S., H. R. Rezaei, P. Taberlet, S. Zudel, S. A. Rafat, H. R. Naghash, M. A. El-Barody, O. Ertugrul, F. Pompanon, & E. Consortium. 2007. Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS ONE 2, e1012. https://doi.org/10.1371/journal.pone.0001012

Naqvi, A. N., J. F. Bukhari, S. M. F. Vahidi, Y. T. Utsunomiya, J. F. Garcia, M. E. Babar, J. L. Han, R. Pichler, & K. Periasamy. 2017. Microsatellite based genetic diversity and mitochondrial DNA D-Loop variation in economically important goat breeds of Pakistan. Small Rumin. Res. 148:62-71. https://doi.org/10.1016/j.smallrumres.2016.12.031

Nei, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.

Othman, O. E. & E. R. Mahfouz. 2016. Genetic biodiversity, affinities and phylogeny of four goat breeds in Egypt. J. Biol. Sci. 16: 86-92. https://doi.org/10.3923/jbs.2016.86.92

Pakpahan, S., W. T. Artama, R. Widayanti, & G. Suparta. 2015. Genetic variations and the origin of native Indonesian goat breeds based on mtDNA D-loop sequences. Asian J. Anim. Sci. 9: 341-350. https://doi.org/10.3923/ajas.2015.341.350

Pekkala, N., K. E. Knott, J. S. Kotiaho, K. Nissinen, & M. Puurtinen. 2014. The effect of inbreeding rate on fitness, inbreeding depression and heterosis over a range of inbreeding coefficients. Evol. Appl. 7:1107-1119. https://doi.org/10.1111/eva.12145

Pereira F., L. Pereira, B. Van Asch, D. G. Bradley, & A. Amorim. 2005. The mtDNA catalogue of all Portuguese autochthonous goat (Capra hircus) breeds: high diversity of female lineages at the western fringe of European distribution. Mol. Ecol. 14:2313-2318. https://doi.org/10.1111/j.1365-294X.2005.02594.x

Permatasari, T., S. Sutopo, & E. Kurnianto. 2014. Inheritance of color of Kejobong goat in Purbalingga Regency Central Java, Indonesia. J. Indonesian Trop. Anim. Agric. 39:137-143. https://doi.org/10.14710/jitaa.39.3.137-143

Piras, D., M. G. Doro, G. Casu, P. M. Melis, S. Vaccargiu, I. Piras, D. Parracciani, R. Stradoni, B. Frongia, G. Lai, W. Cattari, R. Piras, O. Querci, P. Demuro, S. Cui, M. Mancosu, F. Marchiori, R. Cammelli, A. Spiga, S. Sale, F. Atzori, P. P. Loddo, G. Pili, R. Boi, G. Argiolas, P. Mereu, G. G. Leoni, S. Naitana, M. Pirastu, & A. Novelletto. 2012. Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-Loop diversity and reveal specific features of the Sardinian Stock. Plos One. 7:1-11. https://doi.org/10.1371/journal.pone.0030785

Purwantini, D. & Ismoyowati. 2014. Genetic characteristic of Indonesian local ducks based on single nucleotide polymorphism (SNP) analysis in D-loop region mitochondria DNA. J. Anim. Prod. 16:146-155.

Purwantini, D., T. Yuwanta, T. Hartatik, & Ismoyowati. 2013. Polymorphism of D-loop mitochondrial DNA region and phylogenetic in five Indonesian native duck population. Intl. J. Poult. Sci. 12:55-63. https://doi.org/10.3923/ijps.2013.55.63

Royo, L., A. Traoré, H. Tambourá, I. Álvarez, A. Kaboré, I. Fernández, G. Ouédraogo-Sanou, A. Toguyeni, L. Sawadogo & F. Goyache. 2009. Analysis of mitochondrial DNA diversity in Burkina Faso populations confirms the maternal genetic homogeneity of the West African goat. Anim. Genet. 40:344-347. https://doi.org/10.1111/j.1365-2052.2008.01828.x

Saitou, N. & M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.

Sardina, M. T., M. Ballester, J. Marmi, R. Finocchiaro, J. B. C. H. M. van Kaam, B. Portolano, & J. M. Folch. 2006. Phylogenetic analysis of Sicilian goats reveals a new mtDNA lineage. Anim. Genet. 37: 376–378. https://doi.org/10.1111/j.1365-2052.2006.01451.x

Sari, E. M., H. Jianlin, R. R. Noor, C. Sumantri, & E. T. Margawati. 2016. Phylogenetic analysis of Aceh cattle breed if Indonesia through mitochondrial D-loop region. J. Genet. Eng. Biotechnol. 14:227-231. https://doi.org/10.1016/j.jgeb.2015.12.001

Setiaji, A., P. Suparman, & Hartoko. 2013. Produktivitas dan pola warna kambing Kejobong yang dipelihara oleh peternak kelompok dan peternak individu. J. Ilmiah Peternakan. 1:789-795.

Sodiq, A. 2009. Karakterisasi sumber daya kambing lokal khas Kejobong di Kabupaten Purbalingga Propinsi Jawa Tengah. Agripet. 9: 31-37. https://doi.org/10.17969/agripet.v9i1.619

Sulandari, S. & M. S. A. Zein. 2009. Analisis D-loop DNA Mitokondria untuk memposisikan Ayam Hutan Merah dalam domestikasi ayam di Indonesia. Med. Pet. 32:31-39.

Sulandari, S., M. S. A. Zein, & T. Sartika. 2008. Molecular characterization of Indonesian indigenous chickens based on mitochondrial DNA Displacement (D)-loop sequences. Hayati J. Biosci. 15:145-154. https://doi.org/10.4308/hjb.15.4.145

Sultana, S., H. Mannen, & S. Tsuji. 2003. Mitochondrial DNA diversity of Pakistani goats. Anim. Genet. 34:417-421. https://doi.org/10.1046/j.0268-9146.2003.01040.x

Suryani, H. F., E. Purbowati, & E. Kurnianto. 2013. Multivariate analysis on cranium measurements of three breeds of local goat in Central Java. J. Indonesian Trop. Anim. Agric. 38:217-224. https://doi.org/10.14710/jitaa.38.4.217-224

Susanti, R., F. Fibriana, & A. Yuniastuti. 2017a. PCR-RFLP Analysis of D-loop mtDNA in Indonesian domestic waterfowl. Biosaintifika 9:537-544. https://doi.org/10.15294/biosaintifika.v9i3.12177

Susanti, R., R. S. Iswari, F. Fibriana & R. I. Sari. 2017b. Mitochondrial D-loop sequence variation among Central Javanese duck in Indonesia. Acta Sci. Anim. Sci. 39:449-456. https://doi.org/10.4025/actascianimsci.v39i4.34352

Tamura, K., G. Stecher, D. Peterson, A. Filipski, & S. Kumar. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. J. Mol. Biol. Evol. 30:2725-2729. https://doi.org/10.1093/molbev/mst197

Thompson, J. D., D. G. Higgins, & T. J. Gibson. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, Position specific gap penalties and weight matrixchoice. J. Nucleic Acid Res. 22:4673-4680. https://doi.org/10.1093/nar/22.22.4673

Toro M., J. Fernandez, & A. Caballero. 2009. Molecular characterization of breeds and its use in conservation. Livest. Sci. 120:174-95. https://doi.org/10.1016/j.livsci.2008.07.003

Upholt, W. B. & I. B. David. 1977. Mapping of mitochondrial DNA of individual sheep and goats: rapid evolution in the D-loop region. Cell 11:571-583. https://doi.org/10.1016/0092-8674(77)90075-7

Wang, J., Y. L. Chen, X. L. Wang, & Z. X. Yang. 2008. The genetic diversity of seven indigenous Chinese goat breeds. Small Rum. Res. 74:231-237. https://doi.org/10.1016/j.smallrumres.2007.03.007

Wibowo, S. B., E. T. Setiatin, & E. Kurnianto. 2013. The relationship between sperm morphometry and sperm competition in local goats of Central Java, Indonesia. Med. Pet. 36: 179-184. http://dx.doi.org/10.5398/medpet.2013.36.3.179

Wright, L. I., T. Tragenza & D. J. Hosken. 2008. Inbreeding, inbreeding depression and extinction. J. Consv. Genet. 9: 833-834. https://doi.org/10.1007/s10592-007-9405-0

Zein, M. S. A. & S. Sulandari. 2008. Keragaman genetik Ayam Lombok berdasarkan sekuen D-loop DNA mitokondria. Indo. J. Anim. Vet. Sci. 13:307-314.

Zein, M. S. A. & S. Sulandari. 2009. Investigasi asal usul ayam Indonesia menggunakan sekuens Hypervariable-1 D-loop DNA mitokondria. J. Vet. 10:41-49.

Zeuner, F. E. 1963. A History of Domesticated Animals, Hutchinson, London.

Zhao Y. J. Zhang, E. Zhao, X. Zhang, X. Liu, & N. Zhang. 2011. Mitochondrial DNA diversity and origins of domestic goats in Southwest China (excluding Tibet). Small Rum. Res. 95:40-47. https://doi.org/10.1016/j.smallrumres.2010.09.004




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