Iranian Journal of animal Science

Iranian Journal of animal Science

Phylogenetic and Haplogroup analysis of native goats of Iran based on nucleotide sequence of HVR1 region of mitochondrial genome

Document Type : Research Paper

Authors
Maryam Shariat 1
Gholam Reza Dashab 2
Mehdi Vafaye valleh 2
1 Former M.Sc. Student, Animal Breeding and Genetic, Faculty of Agriculture, University of Zabol, Zabol, Iran
2 Associate Professor of Animal Breeding and Genetic, Faculty of Agriculture, University of Zabol, Zabol, Iran
10.22059/ijas.2019.272018.653672
Abstract
Iranian indigenous goats are considered as one of the most valuable genetic reserves and it is important to keep their genetic diversity. The mitochondrial genome in an ecotype and comparing it with other ecotypes can provide an appropriate mesures of the diversity of the population. The purpose of this study was to investigate the genetic structure and phylogenetic relationships analysis of mitochondria HVR1 in four populations of indigenous goats in Iran including of Sistani, Pakestani, adani and Black Lori goats (Each of them has 4 heads) and compare to the other species of goats in the world. Total DNA extraction was performed using phenol-chloroform method and proliferation reaction was performed using a pair of special primers. Proliferation products were sequenced after purification by Sanger method. All of these sequences with17 sequences of the mitochondrial genome of other non Iranian goat ecotypes obtained from the National Center of Biotechnology Information (NCBI) were used for genetic analysis and phylogenetic tree mapping. Studying of HVR1 region of the mitochondrial genome in different goat populations, 123 polymorphic sites and 16 haplotypes were identified. The analysis of molecular variance showed that 15% of variation belongs to between populations and 85% within populations. All Iranian goat populations used in the present study were grouped in the Haplogroup group A, which were commonly found in world ecotypes. The values ​​of the D and Fs statistics of the Tajima test were negative (-2.14 and -9.55 respectively) in the recent study, which may be due to the small size of the sample size. The results of this study showed that HVR1 region of the mitochondrial genome is a suitable tool for genetic studies and Haplogrouping of Iran and Non Iranian goat populations.
Keywords
D-Loop region
Genetic diversity
Phylogenetic relationships
Haplogroup
  1. Alipanah, M., Seydabadi, H. R., Gharan, F. & Rodbari, Z. (2015). Genetic and phylogenetic analysis D-Loop region of mithchondrial genome in Khorasan native turkey. Aniam Science Journal (Pajouhesh and Sazandegi), 107, 119-126. (in Farsi)
  2. Doro, M. G., Piras, D., Leoni, G. G., Casu, G., Vaccargiu, S., Parracciani, D. & Novelletto, A. (2014). Phylogeny and patterns of diversity of goat mtDNA haplogroup A revealed by resequencing complete mitogenomes. PloS One, 9, e95969.
  3. Excoffier, L. (1993). Analysis of molecular variance (AMOVA) version 1.55. Genetics and Biometry Laboratory, University of Geneva, Switzerland. ‏
  4. Huson, D. H. & Steel, M. (2004). Distances that perfectly mislead. Systematic Biology, 53, 327-332.
  5. Jazin, E., Soodyall, H., Jalonen, P., Lindholm, E., Stoneking, M., Gyllensten, U. (1998). Mitochondrial mutationrate revisited: hot spots and polymorphism. Nature Genetics, 18, 109-110.
  6. Joshi, M. B., Rout, P. K., Mandal, A. K., Tyler-Smith, C., Singh, L. & Thangaraj, K. (2004). Phylogeography and origin of Indian domestic goats. Molecular Biology and Evolution, 21(3), 454-462.
  7. Karimi, V., Hedayat Evrigh, N., Seyed Sharifi, R. & Nikbin, S. (2017). Invetigation of genetic structure of Khalkhali goat using mitochondrial genome. Novin Genetic Journal, 12(2), 217-227. (in Farsi)
  8. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of molecular evolution, 16(2), 111-120.
  9. Lie, D. E., Cean, A., Cziszter, L. T., Gavojdian, D., Ivan, A. & 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.
  10. Liu, A. H., Yin, H., Guan, G. Q., Schnittger, L., Liu, Z. J., Ma, M. L. & Ahmed, J. S. (2007). At least two genetically distinct large Babesia species infective to sheep and goats in China. Veterinary Parasitology, 147(3), 246-251.
  11. Liu, Y. P., Cao, S. X., Chen, S. Y., Yao, Y. G. & Liu, T. Z. (2009). Genetic diversity of Chinese domestic goat based on the mitochondrial DNA sequence variation. Journal of Animal Breeding and Genetics, 126(1), 80-89.
  12. Lopez, A. & Bonasora, M. G. (2017). Phylogeography, genetic diversity and population structure in a Patagonian endemic plant. AoB Plants, 16(4), 275.
  13. Luikart, G., Gielly, L., Excoffier, L., Vigne, J. D., Bouvet, J. & Taberlet, P. (2001). Multiple maternal origins and weak phylogeographic structure in domestic goats. In: Proceedings of the National Academy of Sciences, 98, 5927-5932.
  14. Mazdarani, F. H., Akbari, M. T., Fard, R. M. N., Hessari, M. & Pour, K. C. (2014). Molecular identification of Capra hircus in East Chia Sabz, an Iranian pre-pottery Neolithic site, Central Zagros, based on mtDNA. The Journal of Animal & Plant Sciences, 24(3), 945-950.
  15. Moradpour, Z. & Ghasemian, A. (2011). Bioinformatics in simple language. Biological House Publishing, pp. 446-454. (in Farsi)
  16. Mousavizadeh, A., Mohammadabadi, M. R., Torabi, A., Nassiry, M. R., Ghiasi, Esmailizadeh, A. K. (2009). Genetic polymorphism at the growth hormone locus in Iranian Talli goats by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). Iranian Journal of Biotechnology, 7, 51-53. (in Farsi)
  17. Muezzini, F., Afraz, S., Vahid, F. & Toligiyani, A. (2015). Study of mitochondrial DNA diversity in native goat populations of Khalkhal and Qazvini. The 9th National Conference of the Islamic Republic of Iran, p. 66-89. (in Farsi)
  18. Naderi, S., Rezaei, H. R., Taberlet, P., Zundel, S., Rafat, S. A., Naghash, H. R., Elbarody, M. A. A., Ertugrul, O. & Pompanon, F. (2007). Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. Plos One, 2(10), 1-12. (in Farsi)
  19. Pariset, L., Mariotti, M., Gargani, M., Joost, S., Negrini, R., Perez, T. & Valentini, A. (2011). Genetic diversity of sheep breeds from Albania, Greece, and Italy assessed by mitochondrial DNA and nuclear polymorphisms (SNPs). The Scientific World Journal, 11, 1641-1659.
  20. Rout, P., Thangraj, K., Mandal, A. & Roy, R. (2012). Genetic variation and population structure in Jamunapari goats using microsatellites, mitochondrial DNA, and milk protein genes. The Scientific World Journal, 2012, 1-7.
  21. Rozas, J., Sachez-Delbarrio, J. C., Messeguer, X.  & Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496-2497.
  22. Sultana, S., Mannen, H. & Tsuji, S. (2003). Mitochondrial DNA diversity of Pakistani goats. Animal Genetics, 34(6), 417-421.
  23. Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
  24. Tamura, K., Nei, M. & Kumar, S. (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.
  25. Wu, Y. P., Guan, W. J., Zhao, Q. J., He, X. H., Pu, Y. B., Huo, J. H. & Ma, Y. H. (2009). A fine map for maternal lineage analysis by mitochondrial hypervariable region in 12 Chinese goat breeds. Animal Science Journal, 80, 372-380.
  26. Zawadzki, C. H., Pavanelli, C. S. & Langeani, F. (2008). Neoplecostomus (Teleostei: Loricariidae) from the upper Rio Paraná basin, Brazil, with description of three new species. Zootaxa, 1757, 31-48.
  27. Zeder, M. A. & Lapham, H. A. (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.
  28. Zhao, Y., Zhang, J., Zhao, E., Zhang, X., Liu, X. & Zhang, N. (2011). Mitochondrial DNA diversity and origins of domestic goats in Southwest China (excluding Tibet). Small Ruminant Research, 95 (1), 40-47.
Iranian Journal of animal Science
Volume 50, Issue 1
Summer 2019
Pages 35-46

  • Receive Date 22 December 2018
  • Revise Date 02 March 2019
  • Accept Date 13 May 2019