Volume 10, Issue 23 (5-2019)                   rap 2019, 10(23): 133-143 | Back to browse issues page

XML Persian Abstract Print

Download citation:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:

Shariat M, Dashab G R, Vafaye Valleh M. (2019). Comparison of Phylogenetic and Evolutionary of Nucleotide Squences of HVR1 region of Mitochondria genom in Goats and Other Livestock Species. rap. 10(23), 133-143. doi:10.29252/rap.10.23.133
URL: http://rap.sanru.ac.ir/article-1-970-en.html
University of Zabol
Abstract:   (3343 Views)
     Maintaining genomic diversity in goat populations in different parts of Iran is essential for breeding programs, increasing production, survival, resistance to diseases, and various environmental changing conditions. The aim of the present study was to determine the sequence of HVR1 from the mitochondrial genome of Iranian native goats including Sistani, Pakistani, Black and Lorry ecotypes (each of 4 heads), examine the probable variation in these populations, and plotting their phylogen relationship in comparison with some animal species. Total DNA extraction was performed using phenol-chloroform method. The extracted DNA was used as template for proliferation of HVR1 region of mitochondrial genome was used and the obtained bands were sequenced by Sanger method. The nucleotide sequences with 30 sequences from the same region of the mitochondrial genome related to other animal species derived from the National Center for Biotechnology Information (NCBI) were used for genetic analysis and phylogenetic tree mapping. The average of haplotype diversity and nucleotide diversity among species were 0.994 and 0.12891, and, in the ecotypes were 1 and 0.09299, respectively. The numerical value of the replacement rate of dn/ds for the studied ecotypes and other species was calculated at 1.17 and 1.12, respectively, which indicates a positive selection in the process of evolution of this gene. The results of phylogenic tree of nucleotide sequence of HVR1 region were estimated from two major branches and 7 subspaces. Among the studied species, goat ecotypes were similar to sheep species. The genetic and phylogenic analysis of the studied species indicates the distinction and evolutionary path of each species and the HVR1 region can lead to the proper grouping of the species and sub-species that are split from them.
Full-Text [PDF 364 kb]   (1388 Downloads)    
Type of Study: Research | Subject: ژنتیک و اصلاح نژاد دام
Received: 2018/12/1 | Revised: 2019/05/22 | Accepted: 2019/02/19 | Published: 2019/05/22

1. Ahmadian, K., G. Rahimi Mianji, H. Sayahzadeh and H. Deldar. 2017. Assessment of Genetic diversity and phylogenetic relationship of Iranian indigenous chickens based on mitochondrial D-Loop sequences. Research on Animal Production, 8(17): 140-148 (In Persian). [DOI:10.29252/rap.8.17.140]
2. Fajardo, V., I. González, I. López-Calleja, I. Martín, P.E. Hernández, T. García and R. Martín, R. 2006. PCR-RFLP authentication of m eats from red deer (Cervus elaphus), fallow deer (Dama dama), roe deer (Capreolus capreolus), cattle (Bos taurus), sheep (Ovis aries), and goat (Capra hircus). Journal of agricultural and food chemistry, 54(4): 1144-1150. [DOI:10.1021/jf051766r]
3. Guha, S., S.P. Goyal and V.K. Kashyap. 2006. Genomic variation in the mitochondrially encoded cytochrome b (MT‐CYB) and 16S rRNA (MT‐RNR2) genes: characterization of eight endangered Pecoran species. Animal Genetics, 37(3): 262-265. [DOI:10.1111/j.1365-2052.2006.01421.x]
4. Harrison, R.G. 1989. Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends in Ecology & Evolution, 4(1): 6-11. [DOI:10.1016/0169-5347(89)90006-2]
5. Hiendleder, S., K. Mainz, Y. Plante and H. Lewalski. 1998. Analysis of mitochondrial DNA indicates that domestic sheep are derived from two different ancestral maternal sources: no evidence for contributions from urial and argali sheep. Journal of Heredity, 89(2): 113-120. [DOI:10.1093/jhered/89.2.113]
6. Hoda, A., Y. Biçoku and P. Dobi. 2014. Genetic diversity of Albanian goat breeds revealed by mtDNA sequence variation. Biotechnology & Biotechnological Equipment, 28(1): 77-81. [DOI:10.1080/13102818.2014.901672]
7. Joshi, M.B., P.K. Rout, A.K. Mandal, C. Tyler-Smith, L. Singh and K. Thangaraj. 2004. Phylogeography and origin of Indian domestic goats. Molecular Biology and Evolution, 21(3): 454-462. [DOI:10.1093/molbev/msh038]
8. Karimi, V., N. Hedayat Evrigh, R. Seyed Sharifi and S. Nikbin. 2017. Invetigation of genetic structure of Khalkhali goat using mitochondrial genome. Novin Genetic Journal, 12(2); 217-227. (In Persian)
9. Khaldari, M. 2011. Principles of breeding sheep and goats. Jihad University Press, Second edition. (In Persian)
10. Liu, Y.P., S.X. Cao, S.Y. Chen, Y.G. Yao and T.Z. Liu. 2009. Genetic diversity of Chinese domestic goat based on the mitochondrial DNA sequence variation. Journal of Animal Breeding and Genetics, 126(1): 80-89. [DOI:10.1111/j.1439-0388.2008.00737.x]
11. Lopez, A. and M.G. Bonasora. 2017. Phylogeography, genetic diversity and population structure in a Patagonian endemic plant. AoB Plants, 16(4): 275-285. [DOI:10.1093/aobpla/plx017]
12. Mohammadi, P., J. Nazemi Rafie and J. Rostamzadeh. 2018. Evaluation of phylogenetic characteristics of Iranian honeybee (Apis mellifera meda) populations based on mitochondrial ND gene. Research on Animal Production, 9(21): 93-104 (In Persian).
13. Morovati, S. and M. Modaresi. 2005. Study of the HV1 region of mtDNA for use in identity recognition through maternal generations. Journal of Military Medicine, 20: 113-119. (In Persian)
14. Muezzini, F., S. Afraz, F. Vahid and A. Toligiyani. 2015. Study of mitochondrial DNA diversity in native goat populations of Khalkhal and Qazvini. The 9th National Conference of the Islamic Republic of Iran, pp: 66-89 (In Persian).
15. Naderi, S., H.R. Rezaei, P. Taberlet, S. Zundel, S.A. Rafat, H.R. Naghash, M.A.A. Elbarody, O. Ertugrul, F. Pompanon. 2007. Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. Plos One, 2(10): 1-12. [DOI:10.1371/journal.pone.0001012]
16. Nei, M. and S. Kumar. 2000. Molecular evolution and phylogenetics. Oxford university press.
17. Pakpahan S., W. Tunas Artama, R. Widayanti and G. Suparta. 2015. Genetic variations and the origin of native Indonesian goat breeds based on mtDNA D-Loop sequences. Asia Journal of Animal Science, 9: 341-350. [DOI:10.3923/ajas.2015.341.350]
18. Phuphuakrat, A and P. Auewarakul. 2003. Heterogeneity of HIV-1 Rev response element. AIDS Research and Human Retroviruses, 19: 569-574. [DOI:10.1089/088922203322230932]
19. Rozas J., J.C. Sachez-Delbarrio, X. Messeguer and R. Rozas. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19: 2496-2497. [DOI:10.1093/bioinformatics/btg359]
20. Tamura, K., M. Nei and S. Kumar. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Sciences of the United States of America, 101(30): 11030-11035. [DOI:10.1073/pnas.0404206101]
21. Tavakolian, J. 1999. An attitude to the genetic resources of indigenous livestock and poultry. National Animal Science Research Institute, Karaj, Iran. (In Persian)
22. Untergasser, A., I. Cutcutache, T. Koressaar, J. Ye, B.C. Faircloth, M. Remm and S.G. Rozen. 2012. Primer3--new capabilities and interfaces. Nucleic Acids Research, 40(15): e115. [DOI:10.1093/nar/gks596]
23. Zeder, M.A. and H.A. Lapham. 2010. Assessing the reliability of criteria used to identify postcranial bones in sheep, Ovis and goats, Capra. Journal of Archaeological Science, 37(11): 2887-2905. [DOI:10.1016/j.jas.2010.06.032]

Add your comments about this article : Your username or Email:

Send email to the article author

Rights and permissions
Creative Commons License This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

© 2024 CC BY-NC 4.0 | Research On Animal Production

Designed & Developed by : Yektaweb