Browse > Article
http://dx.doi.org/10.5713/ajas.19.0396

Mitochondrial DNA variation and phylogeography of native Mongolian goats  

Ganbold, Onolragchaa (Laboratory of Animal Molecular Genetics, Division of Animal & Dairy Science, Chungnam National University)
Lee, Seung-Hwan (Laboratory of Animal Molecular Genetics, Division of Animal & Dairy Science, Chungnam National University)
Paek, Woon Kee (Daegu National Science Museum of Korea)
Munkhbayar, Munkhbaatar (Department of Biology, Mongolian National University of Education)
Seo, Dongwon (Laboratory of Animal Molecular Genetics, Division of Animal & Dairy Science, Chungnam National University)
Manjula, Prabuddha (Laboratory of Animal Molecular Genetics, Division of Animal & Dairy Science, Chungnam National University)
Khujuu, Tamir (Department of Biology, Mongolian National University of Education)
Purevee, Erdenetushig (Department of Biology, Mongolian National University of Education)
Lee, Jun Heon (Laboratory of Animal Molecular Genetics, Division of Animal & Dairy Science, Chungnam National University)
Publication Information
Asian-Australasian Journal of Animal Sciences / v.33, no.6, 2020 , pp. 902-912 More about this Journal
Abstract
Objective: Mongolia is one of a few countries that supports over 25 million goats, but genetic diversity, demographic history, and the origin of goat populations in Mongolia have not been well studied. This study was conducted to assess the genetic diversity, phylogenetic status and population structure of Mongolian native goats, as well as to discuss their origin together with other foreign breeds from different countries using hypervariable region 1 (HV1) in mtDNA. Methods: In this study, we examined the genetic diversity and phylogenetic status of Mongolian native goat populations using a 452 base-pair long fragment of HVI of mitochondrial DNA from 174 individuals representing 12 populations. In addition, 329 previously published reference sequences from different regions were included in our phylogenetic analyses. Results: Investigated native Mongolian goats displayed relatively high genetic diversities. After sequencing, we found a total of 109 polymorphic sites that defined 137 haplotypes among investigated populations. Of these, haplotype and nucleotide diversities of Mongolian goats were calculated as 0.997±0.001 and 0.0283±0.002, respectively. These haplotypes clearly clustered into four haplogroups (A, B, C, and D), with the predominance of haplogroup A (90.8%). Estimates of pairwise differences (Fst) and the analysis of molecular variance values among goat populations in Mongolia showed low genetic differentiation and weak geographical structure. In addition, Kazakh, Chinese (from Huanghuai and Leizhou), and Arabian (Turkish and Baladi breeds) goats had smaller genetic differentiation compared to Mongolian goats. Conclusion: In summary, we report novel information regarding genetic diversity, population structure, and origin of Mongolian goats. The findings obtained from this study reveal that abundant haplogroups (A to D) occur in goat populations in Mongolia, with high levels of haplotype and nucleotide diversity.
Keywords
Genetic Diversity; Mitochondrial DNA; Native Goats; Phylogenetic Relationships; The Origin;
Citations & Related Records
Times Cited By KSCI : 8  (Citation Analysis)
연도 인용수 순위
1 Porter V. Goats of the world. Ipswich, UK: Farming Press Limited; 1996.
2 Zeder M, Hesse B. The initial domestication of goats (Capra hircus) in the Zagros Mountains 10,000 years ago. Sciences 2000;287:2254-7.   DOI
3 Meadow RH. Animal domestication in the Middle East: a revised view from the eastern margin. In: Possehl G, Oxford and IBH editors. Harappar civilization. New Dehli, India: Harappar Civilization; 1993. p. 295-320.
4 MLS (Mongolian Livestock Sector) [Internet]. Ulaanbaatar, Mongolia: 2010 [cited 2018 Sept 11]. Available at: https://mofa.gov.mn/livestock/index.php?option=com_content&view=category&layout=blog&id=48&Itemid=72&lang=en
5 Ganbold O, Manjula P, Lee SH, et al. Sequence characterization and polymorphism of melanocortin 1 receptor gene in some goat breeds with different coat color of Mongolia. Asian-Australas J Anim Sci 2019;32:939-48. https://doi.org/10.5713/ajas.18.0819   DOI
6 Librado P, Rozas J. DnaSP v5: Software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009; 25:1451-2. https://doi.org/10.1093/bioinformatics/btp187   DOI
7 Lin BZ, Odahara S, Ishida M, et al. Molecular phylogeography and genetic diversity of East Asian goats. Anim Genet 2013; 44:79-85. https://doi.org/10.1111/j.1365-2052.2012.02358.x   DOI
8 Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucleic Acids Symposium Series, 41. Oxford, UK: Oxford University Press; 1999. pp. 95-8.
9 Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673- 80. https://doi.org/10.1093/nar/22.22.4673   DOI
10 Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993;10:512-26. https://doi.org/10.1093/oxfordjournals.molbev.a040023
11 Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870-4. https://doi.org/10.1093/molbev/msw054   DOI
12 Bandelt HJ, Forster P, Rohl A. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 1999;16: 37-48. https://doi.org/10.1093/oxfordjournals.molbev.a026036   DOI
13 Excoffier L, Lischer HEL. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 2010;10:564-7. https://doi.org/10.1111/j.1755-0998.2010.02847.x   DOI
14 Rogers AR, Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 1992;9:552-69. https://doi.org/10.1093/oxfordjournals.molbev.a040727
15 Giuffra EJ, Kijas JMH, Amarger V, Carlborg O, Jeon JT, Andersson L. The origin of the domestic pig: independent domestication and subsequent introgression. Genetics 2000;154: 1785-91.   DOI
16 Harpending HC. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol 1994;66:591-600.
17 Fu YX. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 1997;147:915-25.   DOI
18 Hiendleder S. A low rate of replacement substitutions in two major Ovis aries mitochondrial genomes. Anim Genet 1998; 29:116-22. https://doi.org/10.1046/j.1365-2052.1998.00295.x   DOI
19 Meadows JR, Li K, Kantanen J, et al. Mitochondrial sequence reveals high levels of gene flow between breeds of domestic sheep from Asia and Europe. J Hered 2005;96:494-501. https://doi.org/10.1093/jhered/esi100   DOI
20 Liu J, Ding X, Zeng Y, et al. Genetic diversity and phylogenetic evolution of Tibetan sheep based on mtDNA D-Loop sequences. PloS One 2016;11:e0159308. https://doi.org/10.1002/ece3.3710   DOI
21 Tarekegn GM, Tesfaye K, Mwai OA, et al. Mitochondrial DNA variation reveals maternal origins and demographic dynamics of Ethiopian indigenous goats. Ecol Evol 2018;8:1543-53. https://doi.org/10.1002/ece3.3710   DOI
22 Akis I, Oztabak K, Mengi A, Un C. Mitochondrial DNA diversity of A natolian indigenous domestic goats. J Anim Breed Genet 2014;131:487-95. https://doi.org/10.1111/jbg.12096   DOI
23 Zhao Y, Zhao R, Zhao Z, Xu H, Zhao E, Zhang J. Genetic diversity and molecular phylogeography of Chinese domestic goats by large-scale mitochondrial DNA analysis. Mol Biol Rep 2014;41:3695-704. https://doi.org/10.1007/s11033-014-3234-2   DOI
24 Slatkin M, Hudson RR. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 1991;129:555-62.   DOI
25 Kibegwa FM, Githui KE, Jung'a JO, Badamana MS, Nyamu MN. Mitochondrial DNA variation of indigenous goats in Narok and Isiolo counties of Kenya. J Anim Breed Genet 2016;133:238-47. https://doi.org/10.1111/jbg.12182   DOI
26 Ser-odjav N. The archeology of Mongolia. Studies of Archeological Institute and history of Mongolian Academy of Science. 12th ed. Ulaanbaatar, Mongolia: Munkhyn Useg Press; 1987. pp. 31-42.
27 Chen SY, Su YH, Wu SF, Sha T, Zhang YP. Mitochondrial diversity and phylogeographic structure of Chinese domestic goats. Mol Phylogenet Evol 2005;37:804-14. https://doi.org/10.1016/j.ympev.2005.06.014   DOI
28 Naderi S, Rezaei HR, Taberlet P, et al. Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS One 2007;2:p.e1012. https://doi.org/10.1371/journal.pone.0001012   DOI
29 Takada T, Kikkawa Y, Yonekawa H, Kawakami S, Amano T. Bezoar (Capra aegagrus) is a matriarchal candidate for ancestor of domestic goat (Capra hircus): evidence from the mitochondrial DNA diversity. Biochem Genet 1997;35:315-26. https:// doi.org/10.1023/A:1021869704889   DOI
30 Mannen H, Nagata Y, Tsuji S. Mitochondrial DNA reveal that domestic goat (Capra hircus) are genetically affected by two subspecies of bezoar (Capra aegagurus). Biochem Genet 2001;39:145-54. https://doi.org/10.1023/A:1010266207735   DOI
31 Colli L, Lancioni H, Cardinali I, et al. Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability. BMC Genomics 2015;16:1115. https://doi.org/10.1186/s12864-015-2342-2   DOI
32 Beja-Pereira A, Caramelli D, Lalueza-Fox C, et al. The origin of European cattle: evidence from modern and ancient DNA. Proc Natl Acad Sci 2006;103:8113-8. https://doi.org/10.1073/pnas.0509210103   DOI
33 Mwacharo JM, Bjornstad G, Mobegi V, et al. Mitochondrial DNA reveals multiple introductions of domestic chicken in East Africa. Mol Phylogenet Evol 2011;58:374-82. https://doi.org/10.1016/j.ympev.2010.11.027   DOI
34 Lv FH, Peng WF, Yang J, et al. Mitogenomic meta-analysis identifies two phases of migration in the history of eastern Eurasian sheep. Mol Biol Evol 2015;32:2515-33. https://doi.org/10.1093/molbev/msv139   DOI
35 Touma S, Shimabukuro H, Arakawa A, Oikawa T. Maternal lineage of Okinawa indigenous Agu pig inferred from mitochondrial DNA control region. Asian-Australas J Anim Sci 2019;32:501-7. https://doi.org/10.5713/ajas.18.0378   DOI
36 Tarekegn GM, Ji XY, Bai X, et al. Variations in mitochondrial cytochrome b region among Ethiopian indigenous cattle populations assert Bos taurus maternal origin and historical dynamics. Asian-Australas J Anim Sci 2018;31:1393-400. https://doi.org/10.5713/ajas.17.0596   DOI
37 Teinlek P, Siripattarapravat K, Tirawattanawanich C. Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region. Asian-Australas J Anim Sci 2018;31:804-11. https://doi.org/10.5713/ajas.17.0611   DOI
38 Luikart G, Gielly L, Excoffier L, Vigne JD, Bouvet J, Taberlet P. Multiple maternal origins and weak phylogeographic structure in domestic goats. Proc Natl Acad Sci 2001;98:5927-32. https://doi.org/10.1073/pnas.091591198   DOI
39 Sultana S, Mannen H. Polymorphism and evolutionary profile of mitochondrial DNA control region inferred from the sequences of Pakistani goats. Anim Sci J 2004;75:303-9. https://doi.org/10.1111/j.1740-0929.2004.00190.x   DOI
40 Sardina MT, Ballester M, Marmi J, et al. Phylogenetic analysis of Sicilian goats reveals a new mtDNA lineage. Anim Genet 2006;37:376-8. https://doi.org/10.1111/j.1365-2052.2006.01451.x   DOI
41 Al-Araimi NA, Al-Atiyat RM, Gaafar OM, et al. Maternal genetic diversity and phylogeography of native Arabian goats. Livest Sci 2017;206:88-94. https://doi.org/10.1016/j.livsci. 2017.09.017   DOI
42 NSO (National Statistics Office of Mongolia) [Internet]. Ulaanbaatar, Mongolia: Government III building; 2017 [cited 2018 Sept 2]. Available from: http://www.1212.mn/tables.aspx?TBL_ID=DT_NSO_1001_021V1
43 Ganbold O, Lee SH, Seo D, et al. A review of population genetics research on domestic animals in Mongolia and recommendations for the improvements. J Anim Breed Genom 2018;2: 9-20. https://doi.org/10.12972/jabng.20180016