8954856055505db

برآورد اندازه مؤثر جمعیت گاومیش‌های آبی ایران با استفاده از اطلاعات ژنومی

نوع مقاله: مقاله پژوهشی

نویسندگان

1 استادیار، گروه علوم دامی، دانشکده کشاورزی، دانشگاه ارومیه، ارومیه، ایران

2 استاد، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج، ایران

3 دانشیار، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج، ایران

4 استادیار، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج، ایران

5 استادیار، مؤسسه تحقیقات علوم دامی کشور، سازمان تحقیقات، آموزش و ترویج کشاورزی، کرج، ایران

چکیده

به منظور تعیین اندازه مؤثر جمعیت­های گاومیش ایران از 407 رأس حیوان (260 آذری، 120 خوزستانی و 27 مازندرانی) نمونه­گیری به‌عمل آمد. نمونه­ها بعد از استخراج DNA، با استفاده از آرایه های ژنومیکیAxiom Buffalo Genotyping 90K Array، تعیین ژنوتیپ شدند. اندازه مؤثر جمعیت از 700 تا 4 نسل قبل با استفاده از اطلاعات پیوستگی که برای نمونه تصحیح شده بودند و برای نسل حاضر با استفاده از نرم­افزار (V2)NeEstimator و بر اساس روش هتروزیگوسیتی اضافی، محاسبه گردید. نتایج به­دست آمده برای نسل حاضر نشان می­دهد که اندازه مؤثر جمعیت­های آذری و خوزستانی نسبتاً بالا است و این جمعیت­ها از لحاظ ژنتیکی در معرض انقراض قرار ندارند. ولی شیب بالای کاهش اندازه جمعیت برای این جمعیت­ها نگران­کننده است و بایستی جهت حفظ اندازه مؤثر جمعیت مطلوب و تنوع قابل قبول برای این جمعیت­ها برنامه­ریزی صورت گیرد. همچنین نتایج به‌دست‌آمده برای جمعیت مازندرانی نشان می­دهد این جمعیت از لحاظ ژنتیکی در معرض انقراض قرار دارد. بنابراین بایستی اندازه مؤثر جمعیت به دقت کنترل گردد و نیز با اقتصادی‌کردن تولید و طراحی تلاقی­های مناسب از افزایش هم‌خونی و انقراض ژنتیکی این جمعیت جلوگیری کرده و جمعیت را حفاظت ژنتیکی کرد.

کلیدواژه‌ها


عنوان مقاله [English]

Estimation of effective population size of Iranian water buffalo by genomic data

نویسندگان [English]

  • Mahdi Mokhber 1
  • Mohammad Moradi Shahre Babak 2
  • Mostafa Sadeghi 3
  • Hossein Moradi Shahrbabak 4
  • Javad Rahmani-Nia 5
1 Assistant Professor, Department of Animal Science, Faculty of Agricultural Science, Urmia university, Urmia, Iran
2 Professor, Department of Animal Science, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
3 Associated Professor, Department of Animal Science, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
4 Assistant Professor, Department of Animal Science, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
5 Assistant Professor, Department of Animal Breeding and Genetics, Animal Science Research institute of Iran (ASRI), Karaj, Iran
چکیده [English]

In order to estimate the effective population size (Ne) in Iranian water buffalo blood and hair samples of 407 individual from Azari (N=260), Khuzestani (N=120) and Mazandrani (N=27) buffalo populations were gathered. After DNA extaraction, the samples were genotyped using Axiom® Buffalo Genotyping 90K Array. The Ne was estimated from 700 to 4 generations ago and also for the present generation by linkage disequiblirum data and based on heterozygote-excess method using NeEstimator (V2), respectively. Estimated Ne for Azari, Khuzestani and Mazandarani were calculated 1530, 1375 and 1141, respectively, for 700 generations ago. Ne for the present generation in Azeri, Khuzestani and Mazandarani were estimated 447, 226 and 35, respectively. The Ne for Azeri and Khuzestani were relatively high and these two populations were not endanger to extinction, but their Ne has been declined in the resent generations massively and it is necessary to care about the maintenance of Ne and relatively high diversity for these populations. However, the Mazandarani population is endangered because of low Ne and so it is necessary to carefully monitor their effective population size, improve the profitability of production and planning a suitable mating scheme to control inbreeding and genetically conserve this population.

کلیدواژه‌ها [English]

  • effective population size
  • Linkage disequiblirum
  • Water buffalo
  1. Barton, N. H. & Charlesworth, B. (1998). Why sex and recombination? Science, 281, 1986-1990.
  2. Bohmanova, J., Sargolzaei, M. & Schenkel, F. S. (2010). Characteristics of linkage disequilibrium in North American Holsteins. BMC genomics, 11, 421-432.
  3. Browning, S. R. & Browning, B. L. (2007). Rapid and accurate haplotype phasing and missing-data inference for whole genome association studies by use of localized haplotype clustering. The American Journal of Human Genetics, 81, 1084-1097.
  4. Caballero, A. (1994). Developments in the prediction of effective population size. Heredity, 73(6), 657-679.
  5. Campbell, A. M., Williamson, J., Padula, D. & Sundby, S. (1997). Use PCR & single hair to produce a “DNA Fingerprint”. The American Biology Teacher, 59(3), 172-178.
  6. Charlesworth, B., Nordborg, M. & Charlesworth, D. (1997). The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations. Genetics Research, 70, 155-174.
  7. Colli, L., Milanesi, M., Vajana, E., Iamartino, D. & et al. (2016).  Water buffalo genomic diversity and post domestication migration routes. PAG (Plant and Animal Genome XXIII Conference), Buffalo Session, San Diego, CA (USA).
  8. Crow, J. F. & Kimura, M. (1970). An Introduction to Population Genetics Theory. New York: Harper and Row.
  9. Do, C., Waples, R. S., Peel, D., Macbeth, G. M., Tillett, B. J. & Ovenden, J. R. (2014). NeEstimator V2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources, 14, 209-214.
  10. Flury, C., Tapio, M., Sonstegard, T., Drögemüller, C., Leeb, T., Simianer, H., Hanotte, O. & Rieder, S. (2010). Effective population size of an indigenous Swiss cattle breed estimated from linkage disquisition. Journal of Animal Breeding and Genetics, 127(5), 339-347.
  11. Frankham, R., Bradshaw, C.J.A. & Brook, B.W. (2014). Genetics in conservation and management Revised recommendations for the 50/500 rules, Red List criteria and population viability analyses. Biological Conservation, 170, 56-63.
  12. Hayes, B. J., Visscher, P. M., McPartlan, H. C. & Goddard, M. E. (2003) Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research, 13(4), 635-643.
  13. Hill, W. & Robertson, A. (1968). Linkage disquisition in finite populations. Theoretical and Applied Genetics, 38(6), 226-231.
  14. Kijas, J. W., Lenstra, J. A., Hayes, B., Boitard, S., Neto, L. R. P., San Cristobal, M., Servin, B., McCulloch, R., Whan, V., Gietzen, K. & Paiva, S. (2012). Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biology, 10(2), e1001258. doi:10.1371/journal.pbio.1001258.
  15. Lynch, M., Conery, J. & Burger, R. (1995). Mutation accumulation and the extinction of small populations. The American Naturalist, 146, 489-518.
  16. Meuwissen, T. (2009). Genetic management of small populations: A review. Act Agriculture Sand Section A, 59(2), 71-79.
  17. Nei, M. (1973). Analysis of Gene Diversity in Subdivided Populations. PNAS, Proceedings of the National Academy of Sciences, 70(1), 3321-3323.
  18. Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A. & Reich, D. (2006). Principal components analysis corrects for strati cation in genome-wide association studies. Nature Genetics, 38, 904-909.
  19. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J. & Sham, P. C. (2007). PLINK: a toolset for whole-genome association and population-based linkage analysis. The American Journal of Human Genetics, 81, 559-575.
  20. Robertson, A. (1961). Inbreeding in artificial selection programmes. Genetics Research, 2, 189-194.
  21. Smith, J. M. & Haigh, J. (1974). The hitch-hiking effect of a favourable gene. Genetics Research, 23, 23-35.
  22. Sved, J. (1971). Linkage disquisition and homozygous of chromosome segments in finite populations. Theoretical Population Biology, 2(2), 125-141.
  23. Villa-Angulo, R., Matukumalli, L. K., Gill, C. A., Choi, J., Van-Tassell, C. P. & Grefenstette, J. J. (2009). High-resolution haplotype block structure in the cattle genome. BMC Genetics, 10, 19. doi:10.1186/1471-2156-10-19.
  24. Wang, J. (2005). Estimation of effective population sizes from data on genetic markers. Philosophical Transactions of the Royal Society B: Biological Sciences, 360(1459), 1395-1409.
  25. Wang, J. L. (2004). Application of the one-migrant-per-generation rule to conservation and management. Conservation Biology, 18, 332-343.
  26. Wright, S. (1931). Evolution in Mendelian populations. Genetics, 16, 97-159.
  27. Yang, S., Li, X., Li, K., Fan, B. & Tang, Z. (2014). A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds. BMC Genetics, 15(7), 9. http://www.biomedcentral.com/1471-2156/15/7.