Research Article of International Journal of Animal Research
Estimating the distance of genetic domestic goats in Iran inferred from D-loop region of mitochondrial DNA analysis and origins of candidate native goat ancestor
Sattar. Beig mohammadi 1*, Kian. Pahlevan Afshari 1, and Hamid Reza. Seyedabadi 2
1.Department of Animal Science, Abhar Branch, Islamic Azad University, Abhar, Iran 2.Department of Animal Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research Education and Extension Organization (AREEO),Karaj,Iran
The wild goat “bezoar”(Capra aegagrus) has been considered to be the strongest candidate for the ancestor of the domestic goats (C. hircus) . This article describes the complete sequences of the mitochondrial DNA displacement loop (D-loop) region from Mahabadi goats. The control region (D-loop) is the most variable and non-coding portion of the mitochondrial genome.The genetic diversity and phylogenetic structure was analyzed in Mahabadi goat population by mitochondrial DNA sequences. It is estimated genetic distance between native goat and goat ancestor based on mtDNA. Recent analysis of the most of domestic goat individuals revealed a total of six different monophyletic mitochondrial DNA (mtDNA) haplogroups A, B, C, D, F, and G, with the A haplogroup representing >90% of individuals . Phylogenetic analysis was carried out using hyper variable region 1 (896 bp) obtained form 30 animals. All Mahabadi haplotypes were classified into A haplotype group and revealed remarkably high genetic distances within the population when compared with other goat populations from several places, indicating high genetic variation in the Mahabadi goat. After extracting DNA, displacement loop (D-loop) region of mtDNA was amplified with specific primers using PCR and after purification was sequenced. The phylogenic tree was drawn with the consensus sequence of other similar sequences of different goats breeds and wild goat “bezoar”(Capra aegagrus) obtained from GenBank. InThe phylogenic tree, Mahabadi native goat was clustered with Switzerland, Romania, Austria, Cyprus, Jordan, Spain, Saudi Arabia, Albania , Turkey, Egypt, Kurdi Iran, Malaysia, Kyrgyzstan, Italya and ancestor of native goat breeds. The findings confirmed that Mahabadi goats was closed to Capra aegagrus compared to other domestic goats.
Keywords: genetic diversity, Capra aegagrus, Mahabadi goat, mtDNA, phylogenetic, genetic distance.
How to cite this article:
Sattar. Beig mohammadi, Kian. Pahlevan Afshar, and Hamid Reza. Seyedabadi. Estimating the distance of genetic domestic goats in Iran inferred from D-loop region of mitochondrial DNA analysis and origins of candidate native goat ancestor. International Journal of Animal Research, 2018; 2:20. DOI:10.28933/ijar-2018-07-2801
1. Agaviezor B.O., Adefenwa M.A., Peters S.O., Yakubu A., Ade-bambo O.A., Ozoje M.O., Ikeobi C.O.N., Ilori B.M., Wheto M., Ajayi O.O., Amusan S.A., Okpeku M., De Donato M. and Imumorin I.G. (2012). Genetic diversity analysis of the mito-chondrial D-loop of Nigerian indigenous sheep. Anim. Gen. Resour. 50, 13-20.
2. Arnason U., Gullberg A., Johnsson E. and Ledje C. (1993). The nucleotide sequence of the mitochondrial DNA molecule of the grey seal, Halichoerus grypus and a comparison with the mitochondrial sequences of other true seals. J. Mol. Evol. 37, 323-330.
3. Arnason U., Gullberg A. and Widegren B. (1991). The complete nucleotide sequence of the mitochondrial DNA of the ¢n whale Balaenoptera physalus. J. Mol. Evol. 33, 556-568.
4. Ameur A., Stewart J.B., Freyer C., Hagstro E., Ingman M., Ran N., Larsson G. and Gyllensten U. (2011). Ultra-deep sequenc-ing of mouse mitochondrial DNA: mutational patterns and their origins. PLoS Gent. 7, 1-15.
5. Anderson S., DeBruijin M.H.L., Colson A.R., Eperon I.C., Sanger F. and Young I.G. (1982). Complete sequence of bovine mito-chondrial DNA conserved features of the mammalian mito-chondrial genome. J. Mol. Biol. 156, 683-692.
6. Brown W.M., George M.J. and Wilson AC. (1979). Rapid evolu-tion of animal mitochondrial DNA. Proc. Nat. Acad. Sci. USA. 76, 1967-1971.
7. Chen S.Y., Su Y.H., Wu S.F., Sha T. and Zhang Y.P. (2005). Mi-tochondrial diversity and phylogeographic structure of Chi-nese domestic goats. Mol. Phylogenet. Evol. 73, 804-814.
8. Çinar Kul B. and Ertugrul O. (2011). mtDNA diversity and phy-logeography of some Turkish native goat breeds. Ankara Üniv. Vet. Fak. Derg. 58, 129-134.
9. Cozzi M.C., Strillacci M.G., Valianti P., Bighignoli B., Cancedda M. and Zanotti M. (2004). Mitochondrial D-loop sequence variation among Italian horse breeds. Genet. Sel. Evol. 36, 663-672.
10. Foren D.R., Hixson J.E. and Brown W.M. (1988). Comparisons of ape and human sequences that regulate mitochondrial DNA transcription and D-loop DNA synthesis. Nucleic Acids. Res. 16, 5841-5861.
11. Ghivizzani S.C., Madsen C.S. and Hauswirth W.M. (1993). In organello footprinting: analysis of protein binding at regula-tory regions in bovine mitochondrial DNA. J. Biol. Chem. 268, 8675-8682.
12. Hall T.A. (1999). Bio edit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids. Symp. Ser. 41, 95-98.
13. Hoda A., Bicoku Y. and Dobi P. (2014). Genetic diversity of Al-banian goat breeds revealed by mtDNA sequence variation. Biotechnol. Biotec. Equip. 28, 77-81.
14. oque M.R., Choi N.R., Sultana H., Kang B.S., Heo K.N., Hong S.K., Jo C. and Lee J.H. (2013). Phylogenetic analysis of a privately-owned Korean Native chicken population using mtDNA D-loop variations. Asian-Australas J. Anim. Sci. 26, 157-162.
15. Ilie D.E., Cean A., Cziszter L.T., Gavojdian D., Ivan A. and Kusza S. (2015). Microsatellite and mitochondrial DNA study of native eastern European cattle populations: the case of the Romanian Grey. PLoS One. 10, 1-18.
16. Joshi M.B., Rout P.K., Mandal A.K., Tyler-Smith C., Singh L. and Thangaraj K. (2004). Phylogeography and origin of Indian domestic goats. Mol. Biol. Evol. 21, 454-462.
17. Kumar S., Tamura K., Jakobsen I.B. and Nei M. (2004). MEGA3.1: Molecular Evolutionary Genetics Analysis Soft-ware. Arizona State University Press, Tempe, USA.
18. i K.Y., Li K.T., Cheng C.C., Chen C.H., Hung C.Y. and Ju Y.T. (2014). A genetic analysis of Taoyuan pig and its phylogenetic relationship to Eurasian pig breeds. Asian-Australas J. Anim. Sci. 28, 457-466.
19. Liu Z.G., Lei C.Z., Luo J., Ding C., Chen G.H., Chang H., Wang K.H., Liu X.X., Zhang X.Y., Xiao X.J. and Wu S.L. (2006). Genetic variability of mtDNA sequences in Chinese native chicken breeds. Asian-Australas J. Anim. Sci. 7, 903-909.
20. Luikart G., Gielly L., Excoffier L., Vigne J.D., Bouvet J. and Taberlet P. (2001). Multiple maternal origins and weak phy-logeographic structure in domestic goats. Proc. Nat. Acad. Sci. USA. 98, 5927-5932.
21. Mignotte F., Gueride M., Champagne A.M. and Mounolou J.C. (1990). Direct repeats in the non-coding region of mitochondrial DNA. Involvement in the generation of intra and inter-individual heterogeneity. European J. Biochem. 194, 561-571.
22. Moradi M.H., Rostamzadeh J., Rashidi A., Vahabi K. and Farah-mand H. (2014). Analysis of genetic diversity in Iranian mo-hair goat and its color types using Inter Simple Sequence Re-peat (ISSR) markers. Agric. Commod. 2, 55-62.
23. Naderi S., Rezaei H.R., Taberlet P., Zundel S., Rafat S.A., Na-ghash H.R., Elbarody M.A.A., Ertugrul O. and Pompanon F. (2007). Large-scale mitochondrial DNA analysis of the do-mestic goat reveals six haplogroups with high diversity. PloS One. 2, 1-10.
24. Pakpahan S., Tunas Artama W., Widayanti R. and Suparta G. (2015). Genetic variations and the origin of native Indonesian goat breeds based on mtDNA D-Loop sequences. Asia J. Anim. Sci. 9, 341-350.
25. Rozas J., Sachez-Delbarrio J.C., Messeguer X. and Rozas R. (2003). DnaSP, DNA polymorphism analyses by the coales-cent and other methods. Bioinformatics. 19, 2496-2497.
26. Saccone C., Pesole G. and Sbisa E. (1991). The main regulatory region of mammalian mitochondrial DNA: structure function model and evolutionary pattern. J. Mol. Evol. 33, 83-91.
27. Saitou N. and Nei M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
28. Sultana S., Mannen H. and Tsuji S. (2003). Mitochondrial DNA diversity of Pakistani goats. Anim. Genet. 34, 417-421.
29. Taberlet P., Valentini A., Rezaei H.R., Naderi S., Pompanon F., Negrini R. and Ajmone-Marsan P. (2008). Are cattle, sheep, and goats endangered species. Mol. Ecol. 17, 275-284.
30. Tamura K. and Nei M. (1993). Estimation of the number of nu-cleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512-526.
31. Wilson A.C., Cann R.L., Carr S.M., George M., Gyllensten U.B., Helm-Bychowski K.M., Higuchi R.J., Palumbi S.R., PragerE.M., Sage R.D. and Stoneking M. (1985). Mitochon-drial DNA and two perspectives on evolutionary genetics. Biol. J. Linn. Soc. 26, 375-400.
32. Xu X., Gullberg A. and Arnason U. (1996). The complete mito-chondrial DNA (mtDNA) of the donkey and mtDNA compari-sons among four closely related mammalian species pairs. J. Mol. Evol. 43, 438-446.
33. Zernekova C., Kott T. and Majzlik I. (2013). Mitochondrial D-loop sequence variation among Hucul horse. Czech J. Anim. Sci. 58, 437-442.
34. Naderi S., Rezaei H.R., Taberlet P., Zundel S., Rafat S.A., Naghash H.R., el-Barody M.A., Ertugrul O., Pompanon F., Econogene C. (2007). Largescale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS ONE 2, e1012.
35. Parma P., Feligini M., Greppi G., Enne G. (2003). Thecomplete nucleotide sequence of goat (Caprahircus) mitochondrial genome. DNA Seq., 14, 199-203.
36. Luikart G., Gielly L., Excoffer L., Vigne J.D., BouvetJ., Taberlet P. (2001). Multiple maternal originsand weak phylogeographic structure in domesticgoats. Proceedings of the National Academy of Sciences USA 98, 5927-32.
37. Saitou N and Nei M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4: 406-425.
38. Amer, S.A.M. (2014). Mitochondrial DNA Variability among Some. Saudi Arabian Goat Breeds. British Biotechnology Journal. 4(8): 877-882.
39. Amills M., Ramirez O., Tomas A., Badaoui B., Marmi J.,Acosta J., Sanchez A., Capote J. (2009). Mitochondrial DNA diversity and origins of South and Central American goats. Anim. Genet., 40, 315-322.
40. Avise, J. C. (1994). Molecular markers, natural history and evolution. Chapman & Hall, New York, N.Y. Boyazoglu J., Hatziminaoglou I., Morand-Fehr P. (2005). The role of the goat in society: past, present and per spectives for the future. SmallRumin. Res. 60, 13-23.
41. Esposti M.D., Crimi M., Ghelli A., Patarnello T., cytochrome b: evolution and structure of theprotein. In: Biochim. Biophys. Acta 1143(3). 243-271.
42. Howell N. (1989). Evolutionary conservation of protein regions in the protonmotive cytochrome b and their possible roles in redox catalysis. In: J. Mol. Evol. 29(2): 157- 169.
43. Librado, P. and J. Rozas (2009). DnaSP v5: Asoftware for comprehensive analysis ofDNA polymorphism data. Bioinformatics, 25: 1451-1452.