تجزیه و تحلیل ژنتیکی و فیلوژنتیکی بر اساس ناحیه HVR I D-loop میتوکندری سه نژاد گوسفند بومی ایران (تالشی، شال و ماکویی)

نوع مقاله : مقاله کامل

نویسندگان

گروه علوم دامی، دانشکده علوم دامی و صنایع غذایی، دانشگاه علوم کشاورزی و منابع طبیعی خوزستان، ملاثانی، ایران

چکیده

خلوص ژنتیکی نژادهای گوسفند با توجه به تلاقی‌های کنترل نشده رو به کاهش است به همین علت حفظ تنوع زیستی در نژادهای بومی به عنوان یک سرمایه ملی ضرورت دارد. بنابراین هدف از انجام این پژوهش بررسی تنوع ژنتیکی و فیلوژنتیکی ناحیه HVR I D-loop ژنوم میتوکندری، بین سه نژاد گوسفند تالشی، شال و ماکویی بود. جهت انجام آنالیزها از توالی‌های ناحیه D-loop میتوکندری سه نژاد تالشی، شال و ماکویی ذخیره شده در بانک اطلاعاتی NCBI استفاده شد. تنوع نوکلئوتیدی برای نژاد تالشی، شال و ماکویی به ترتیب 04160/0، 04552/0 و 04422/0 و تنوع هاپلوتایپی در هر سه نژاد 00/1 برآورد شد. همچنین نتایج تجزیه واریانس مولکولی (AMOVA) حاکی از آن بود که تنوع درون جمعیت‌ها 100 درصد و تنوع بین جمعیت‌ها صفر درصد بود. این نتایج بیانگر وجود تنوع بسیار بالا در این نژادها می‌باشد. محاسبه D تاجیمای منفی برای نژاد تالشی بیان‌کننده این موضوع است که جمعیت نژاد تالشی بعد از گذراندن یک تنگنای ژنتیکی در حال گسترش است و انتخاب جهت‌دار در حال انجام است. در حالی که محاسبه D تاجیمای مثبت برای دو نژاد شال و ماکویی نشان می‌دهد که این دو جمعیت در حال گزینش متعادل‌کننده هستند. با رسم درخت فیلوژنتیک به روش NJ مشخص گردید هر سه نژاد گوسفند در گروه هاپلوتایپی D قرار دارند. از قرارگیری این نژادها در گروه نژادهای قفقاز و ترکیه می‌توان نتیجه گرفت که این سه نژاد از نژادهای قدیمی و باستانی هستند و باید جهت حفظ این سرمایه‌های ملی تلاش بیشتری کرد.

کلیدواژه‌ها


عنوان مقاله [English]

Genetic and phylogenetic analysis of mitochondrial D-loop HVR I region in three breeds of native sheep Iran (Taleshi, Shal and Makui)

نویسندگان [English]

  • M Nazari
  • Gh Mohamadi Ahvazi
Department of Animal Science, Faculty of Animal science and Food Technology, Agricultural Science and Natural Resources University of Khuzestan, Mollasani, Ahvaz, Iran
چکیده [English]

The genetic purity of sheep breeds is declining due to uncontrolled crossbreeding, so it is essential to preserve biodiversity in native breeds as a national asset. Therefore, the purpose of this study was to investigate the genetic and phylogenetic diversity of the mitochondrial HVR I region between the three Taleshi, Makui and Shal breeds. For this purpose, HVR I sequences of these three breeds were downloaded from NCBI database. Nucleotide diversity for Taleshi, Shawl and Makui breeds calculated 0.0416, 0.04552 and 0.04422, respectively, and haplotype diversity in all three breeds was estimated to be 1.00. In addition, the results of molecular analysis of variance (AMOVA) showed that the diversity within populations was about %100 and in fact the total diversity was included and the diversity between populations was %0. These results indicated high genetic variation in three sheep breeds. Negative Tajima''s D for Taleshi breed indicated that the this population is expanding after going through a recent bottleneck and selection sweep is in progress, while positive Tajima''s D for shawl and Makui breeds demonstrated that these two populations are balancing selection. The NJ phylogenetic test results indicated that all three breeds of sheep were classified into haplotype D. From the classification of these breeds with the Caucasian and Turkish breeds in one branch, it can be concluded that these three breeds are the ancient breeds of sheep and more efforts should be made to preserve these national assets.
 

کلیدواژه‌ها [English]

  • Genetic diversity
  • HVR I
  • phylogenetic tree
  • mitochondrial genome
  • sheep
1. Balloux, F. and Lugon, M. N. 2002. The estimate of population diffrention with microsatellite markers. Molecular Ecology. 11, 155-165.
2. Chessa, B., Pereira, F., Arnaud, F., Amorim, A., Goyache, F., Mainland, I., Kao, R. R., Pemberton, J. M., Beraldi, D., Stear, M. J., Alberti, A., Pittau, M., Iannuzzi, L., Banabazi, M. H., Kazwala, R. R., Zhang, Y. P., Arranz, J. J., Ali, B. A., Wang, Z., Uzun, M., Dione, M. M., Olsaker, I., Holm, L. E., Saarma, U., Ahmad, S., Marzanov, N., Eythorsdottir, E., Holland, M. J., Ajmone-Marsan, P., Bruford, M. W., Kantanen, J., Spencer, T. E. and Palmarini, M. 2009. Revealing the history of sheep domestication using retrovirus integrations. Science. 324:532–536.
3. Colombo, F., Marchisio, E., Pizzini, A. and Cantoni, C. 2004. Identification of the goose species (Anser ancer) in Italian mortara salami by DNA sequencing and a polymerase chain reaction with an original primer pair. Journal of Meat Science. 61: 261-294.
4. Freeland, J. 2010. Molecular ecology. Translation: Mansoura Malekian. Mashhad University Jihad Publications, Mashhad. Pp.108-104. (In Farsi).
5. Galtier, N., Nabholz, B., Glemin, S. and Hurst G. D. D. 2009. Mitochondrial DNA as a marker of molecular diversity. Molecular Ecology. 18: 4541-4550.
6. Harley, E. H., Baumgarten, I., Cunningham, J. and O’Ryan, C. 2005. Genetic variation and population structure inremnant populations of black rhinoceros, Diceros bicornis in Africa. Molecular Ecology. vol. 14, no. 10, pp. 2981–2990.
7. Hedrik, P.W. 1999. Genetics of population. Second edition. Jones and Bartlett publshers. Sudbury. MA.USA.                                        
8. Hiendleder, S., Mainz, K., Plante, Y. and Lewalski, H. 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: 113–120. 
9. Huson, D. H. and Steel, M. 2004. Distances that perfectly mislead. Systematic Biology. 53: 327-332.
10. Jazin, E., Soodyall, H., Jalonen, P., Lindholm, E., Stoneking, M. and Gyllensten, U. 1998. Mitochondrial mutation rate revisited: hot spots and polymorphism. Nature Genetics. 18: 109-110.  
11. Lv, F. H., Peng, W. F., Yang, J., Zhao, Y. X., Li, W. R., Liu, M. J., Ma, Y. H., Zhao, Q. J., Yang, G. L., Wang, F., Li, J. Q., Liu, Y. G., Shen, Z. Q., Zhao, Sh. G., Hehua, E., Gorkhali, N. A., Vahidi, F., Muladno, M., Naqvi, A. N., Tabell, J., Touru, T. L., Bruford, M. W., Kantanen, J., Han, J. L. and Li, M. H. 2016. Mitogenomic Meta-Analysis Identifies Two Phases of Migration in the History of Eastern Eurasian Sheep. Molecular. Biology. Evolution. 32(10):2515–2533.      
12. Mohammad hashemi, A., Pirani, N., Nassiri, M.R., Abbassi Daloii, T. and Baghban Kohnegroz, B. 2012. Studying the Partially Sequenced mtDNA Hypervariable Region 1 (HVR1) of Iranian Moghani Sheep. Annals Biological Research. 3: 2906-2910. 
13. Mohammadi Ahwazi, G., Nazari, M., Mohammadabadi, M. R. and Heidari, R. 2019. Genetic and phylogenetic analysis of mitochondrial HVR1 region in three breeds of Iranian sheep. Modern Genetics Journal. 14: 209-217. (In Farsi).
14. Murray, B. W. 1996. The estimation of genetic distance and population substructure from microsatellite alleles frequency data. Canada department biology. 40: 112-114.  
15. Peakall, R. and Smouse, P.E. 2006. Gen AlEx 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology. Notes. 6: 288–295.
16. Pirkhzaranian, Z., Razmakbir, M. And Nazifi, N. 2017. Genetic and phylogenetic analysis of part of the mitochondrial genome control region in Zandi sheep. Journal of Agricultural Biotechnology. Vol. 9: No. 3. (In Farsi).
17. Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J. C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S. E. and Sánchez-Gracia, A. 2017. DnaSP 6: DNA Sequence Polymorphism Analysis of Large Datasets. Molecular Biology Evolution. 34 (12): 3299-3302.
18. Selionova, M. I., A.-M. M. Aibazov, T. V. Mamontova, I. A. Stolpovsky, S. V. Beketov, S. N. Petrov, V. R. Kharzinova, A. V. Dotsev and N. A. Zinovieva. 2021. Characteristics of the Allele Pool and the Genetic Differentiation of Goats of Different Breeds and their Wild Relatives by Str-Markers. Archives of Razi Institute. 76: 1351-1362.
19. Sajjadi Zarjani, Z., Bahraini Behzadi, M. R. And Fardaei, M. 2016. Genetic and phylogenetic analysis of HVR1 region of mitochondrial genome in six Iranian sheep breeds. Journal of Ruminant Research. Vol. 4. No. 3. (In Farsi).
20. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123 (3): 585–95.
21. Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology Evolution. 30: 2725-2729.
22. Tapio, M., Marzanov, N., Ozerov, M., Cinkulov, M., Gonzarenko, G., Kiselyova, T., Murawski, M., Viinalass, H. and Kantanen, J. 2006. Sheep mitochondrial DNA variation in European, Caucasian, and Central Asian areas. Molecular Biology and Evolution. 23: 1776–1783.
23. Valizadeh, R. 2010. Sheep and goat breeding. Ferdowsi University of Mashhad Publications, Mashhad. pp. 59, 61 and 62. (In Farsi).
24. Wallce, D. C. 1992. Mitochondrial genetics aparadigm for aging and degenertive diseases. Science. 256: 628-632.
25. Weir, B. S. 1996. Genetic data analysis: methods for discrete population genetic data. Sinauer associations, INC.       
26. Wrigth, S. 1978. Evolution and the Genetics of Population. Variability Within and Among Natural Populations. The University of Chicago Press, Chicago.  
27. Zeder, M. A. 2008. Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact. Proceedings of the National Academy of Sciences of the United States of America. 105: 11597– 11604. 
28. Zhang, D. X. and Hewitt, G. M. 2003. Nuclear DNA analyses in genetic studies of papulations: practice, problems and prospets. Molecular Ecology. 12: 563-584.