| تعداد نشریات | 286 |
| تعداد نشریات سازمان | 84 |
| تعداد شماره‌ها | 2,845 |
| تعداد مقالات | 32,297 |
| تعداد مشاهده مقاله | 41,381,708 |
| تعداد دریافت فایل اصل مقاله | 18,556,653 |
بررسی تنوع ژنتیکی گاوهای بومی ایران و هلشتاین با استفاده از اطلاعات ژنومی | ||
| علوم دامی | ||
| دوره 36، شماره 138، خرداد 1402، صفحه 87-98 اصل مقاله (1.99 M) | ||
| نوع مقاله: مقاله پژوهشی | ||
| شناسه دیجیتال (DOI): 10.22092/asj.2022.357456.2201 | ||
| نویسندگان | ||
| حسین مرادی شهر بابک* 1؛ پریسا بیابانی1؛ حسن مهربانی یگانه1؛ مهدی مخبر2 | ||
| 1گروه علوم دامی، دانشکده کشاورزی و منابع طبیعی، دانشگاه تهران، | ||
| 2گروه علوم دامی، دانشکده کشاورزی، دانشگاه ارومیه. | ||
| چکیده | ||
| در مطالعه‌ی حاضر، از اطلاعات ژنومی 590 رأس گاو شامل گاوهای بومی سرابی، کرمانی، کردی، تالشی، سیستانی، نجدی، مازندرانی و توده نژادی پارس، آمیخته‌های بومی شمال غرب کشور، هلشتاین ایران، هلشتاین فرانسه و هلشتاین ایرلند استفاده شد.کنترل کیفی با استفاده از نرم‌افزار Plink انجام شد. به-طوری‌که جایگاه‌ها و افراد با بیش از 5 درصد ژنوتیپ ازدست‌رفته، نشانگرهای SNP با MAF کمتر از 1 درصد و نیز نشانگرهای SNP که بر اساس تصحیح بنفرونی خارج از تعادل هاردی – واینبرگ بودند، حذف شدند. درنهایت تعداد 509 رأس حیوان با تعداد 13512 نشانگر SNP برای مطالعات ساختار جمعیت مورداستفاده قرار گرفت. بررسی و شناسایی گروه‌های ژنتیکی با استفاده از آنالیز تحلیل مؤلفه‌های اصلی (PCA) و توسط پکیج آماری GenABEL انجام شد. اطلاعات مربوط به آنالیز PCA و اختلاط جمعیتی نشان داد که جمعیت‌های موردمطالعه در چهار گروه مجزا شامل گاوهای سرابی خالص در گروه اول، آمیخته‌های بومی شمال غرب کشور در گروه دوم، جمعیت‌های اصیل هلشتاین در گروه سوم و نژادهای بومی ایران در گروه چهارم قرار دارند. همچنین نتایج آنالیز شاخص تمایز جمعیتی (FST) نشان‌دهنده دامنه‌ی وسیعی از تمایز بین جمعیت‌ها از 180/0 بین نژادهای سیستانی و کردی تا 007/0 و 004/0 در بین نژادهای هلشتاین ایران و ایرلند با هلشتاین فرانسه بود. بررسی تمایز جمعیتی دام‌های بومی با هلشتاین اصیل حاکی از آن بود که نژاد سیستانی بالاترین تمایز را با نژادهای مختلف هلشتاین (128/0 تا 138/0) دارد و با اختلاف اندک نسبت به سایر نژادها، نژاد کردی و مازندرانی کمترین تمایز ژنتیکی را با جمعیت‌های هلشتاین موردمطالعه داشتند. | ||
| کلیدواژه‌ها | ||
| تنوع ژنتیکی؛ تمایز جمعیتی؛ گاو هلشتاین؛ آمیخته‌های بومی | ||
| عنوان مقاله [English] | ||
| Investigating the genetic diversity of Iranian native and Holstein cattle breeds using genomic data | ||
| نویسندگان [English] | ||
| Hossein Moradi Shahrebabak1؛ Parisa Biabani1؛ Hasak Mehrbani Yeganeh1؛ Mahdi Mokhber2 | ||
| 1assistant professor/Department of Animal Sciences, University College of Agriculture and Natural Resources, University of Tehran | ||
| 2Assistant Professor, Department of Animal Science, Faculty of Agricultural Science, Urmia university, Urmia, Iran. | ||
| چکیده [English] | ||
| In this study, genomic data of 590 cattle were used including native breeds of Sarabi, Kermani, Kurdi, Talashi, Sistani, Najdi, Mazandarani and Pars, crossbred from northwest of Iran, Holstein populations from Iran, France and Ireland. Quality control and data filtration were performed using Plink 1.9 software. After this quality control, individuals and SNPs with call rate below 0.95%, SNP makers with minor allele frequency (MAF) > 0.01%, divergence from Hardy-Weinberg Equilibrium were excluded. This procedure yielded 509 individuals with 13512 SNP marker. Then filtered data were used to genetic diversity and clustering analysis. Identification of genetic groups were performed using PCA analysis data by GenABEL software. PCA and ADMIXTURE analysis showed that studied populations are in 4 separate categories including purebred Sarabi population in the first group, crossbred from northwest of Iran in the second group, purebred Holstein populations in the third group and native breeds of Iran were in the fourth group. Further details of demographic differentiation were identified by Weir and Cockerham's fixation index. The range of differentiation in the present study varied from 0.180 between Sistani and Kurdish breeds to 0.007 to 0.004 between the Iran Holstein breed and Ireland with France Holstein breeds. The results showed that the highest difference between indigenous and Holstein breeds related to Sistani breed that had the highest difference with different Holstein breeds (0.128 to 0.138). With slight differences from other Iranian indigenous breeds, the Kurdish and Mazandaran breeds had the smallest genetic differences with the studied Holstein populations. | ||
| کلیدواژه‌ها [English] | ||
| Genetic Diversity, Fixation Index, Holstein Cattle, Indigenous Crossbred | ||
| مراجع | ||
|
Alexander, D.H., Lange, K. (2011). Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics 12:246. Alexander, D.H., Novembre, J. and Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research. 19: 1655–1664. Al-Mamun, H.A., Clark, S.A., Kwan, P. and Gondro, C. (2015). Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genetics Selection Evolution. 47(1): 1-14. Ben Jemaa, S., Boussaha, M., Ben Mehdi, M., Lee, J.H. and Lee, S.H. (2015). Genome-wide insights into population structure and genetic history of tunisian local cattle using the illumina bovinesnp50 beadchip. BMC Genomics. 16: 67.7. Bett, R.C., Okeyo, M.A., Malmfors, B., Johansson, K., Agaba, M., Kugonza, D.R., Bhuiyan, A.K.F.H., Mariante, A.S., Mujibi, F.D. and Philipsson, J. (2013). Cattle breeds: extinction or quasi-extant? Resources. 2(3): 335-357. Bollongino, R., Burger, J., Powell, A., Mashkour, M., Vigne, J.D. and Thomas, MG. (2012). Modern taurine cattle descended from small number of Near-Eastern founders. Molecular Biology and Evolution. 29: 2101–2104. Cornélis, D., Melletti, M., Korte, L., Ryan, S. J., Mirabile, M., Prin, T. and Prin, H.H.T. (2014). Ecology, Evolution and Behaviour of Wild Cattle. Implications for Conservation. Cambridge University Press Publication. Cambridge. UK. pp: 326-372. Decker, J.E., McKay, S.D., Rolf, M.M., Kim, J., Molina Alcala, A., Sonstegard, T.S. and et al. ( 2014). Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genetics. 10: e1004254. FAO. (2018). Food and agriculture and organization of the united nations. Retrieved from www.fao.org/home/en history of French cattle from dense SNP data on 47 worldwide breeds. PloS one. 5(9), p.e13038. Groeneveld, L.F., Lenstra, J.A., Eding, H., Toro, M.A., Scherf, B., Pilling, D. ET AL. (2010). Genetic diversity in farm animals: A review. Animal Genetics. 41: 6–31. Hole, F. (2004). Neolithic Age in Iran. In: Encyclopaedia Iranica. onlineth ed. New York: Columbia University. Jarrige, J.F. Mehrgarh Neolithic. In Proceedings of the International Seminar on the “First Farmers in Global Perspective”, Lucknow, India, 18–20 January 2006; pp. 135–154. Jombart, T., Devillard, S. and Balloux, F. (2010). Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics.11: 1-15. Karimi, K. (2017). Investigation of the Population Structure in Iranian Native Cattle using Discriminant Analysis of Principal Components. Research on Animal Production. 8 (17):184-193. Karimi, K., Koshkoiyeh, A.E., Fozi, M.A., Porto-Neto, L.R. and Gondro, C. (2016a). Prioritization for conservation of Iranian native cattle breeds based on genome-wide SNP data. Conservation Genetics. 17(1): 77-89. Karimi, K., Strucken, E. M., Moghaddar, N., Ferdosi, M. H., Esmailizadeh, A. and Gondro, C. (2016b). Local and global patterns of admixture and population structure in Iranian native cattle. BMC genetics. 17(1): 1-14. Kijas, J.W., Ortiz, J.S., McCulloch, R., James, A., Brice, B., Swain, B. and et al. (2013). Genetic diversity and investigation of polledness in divergent goat populations using 52 088 SNPs. Animal Genetics. 44(3): 325-335. Kukučková, V., Moravčíková, N., Ferenčaković, M., Simčič, M., Mészáros, G., Sölkner, J., Trakovická, A., Kadlečík, O., Curik, I. and Kasarda, R. (2017). Genomic characterization of Pinzgau cattle: genetic conservation and breeding perspectives. Conservation Genetics, 18(4): 893-910. Mastrangelo, S., Sardina, M.T., Tolone, M., Di Gerlando, R., Sutera, A.M., Fontanesi, L. and Portolano, B. (2018). Genome-wide identification of runs of homozygosity islands and associated genes in local dairy cattle breeds. Animal. 12(12): 2480-2488. Medugorac, I., Medugorac, A., Russ, I., Veit-Kensch, C.E., Taberlet, P., Luntz, B. ET AL. (2009). Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size. Molecular Ecology. 18: 3394–3410. Nei, M. (1978) Estimation of average heterozygosity and genetic distance from small number of individuals. Genetics. 89: 583–90. Papachristou, D., Koutsouli, P., Laliotis, G.P., Kunz, E., Upadhyay, M., Seichter, D., Russ, I., Gjoko, B., Kostaras, N., Bizelis, I. and Medugorac, I. (2020). Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations. Genetics Selection Evolution. 52(1): 1-23. Pitt, D., Sevane, N., Nicolazzi, E.L., MacHugh, D.E., Park, S., Colli, L., Martinez, R., Bruford, M.W. and Orozco-terWengel, P. (2018). Domestication of cattle: Two or threeevents? Evolutionary applications, 12 (1), 123–136. Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A. and Reich, D. (2006). Principal components analysis corrects for stratification in genome-wide association studies. Nature genetics. 38(8): 904-909. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A.R., Bender, D. and et al. (2007). PLINK: a toolset for whole-genome association and population-based linkage analysis. The American Journal of Human Genetics. 81: 559–575. Qanbari, S., Pimentel, E.C.G., Tetens, J., Thaller, G., Lichtner, P., Sharifi, A.R. and Simianer, H., (2011). A genome‐wide scan for signatures of recent selection in Holstein cattle. Animal genetics. 41(4): 377-389. R Core Team (2020) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna. Available at URL: http://www.r-project.org/index.html Reynolds, J., Weir, B.S. and Cockerham, C.C. (1983) Estimation of the coancestry coefficient basis for a short-term genetic distance. Genetics. 105: 767–779. Ringner, M. (2008). What is principal component analysis? Nature Biotechnology. 26: 303-304. Rothammer, S., Seichter, D., Förster, M. and Medugorac, I. (2013). A genome-wide scan for signatures of differential artificial selection in ten cattle breeds. BMC genomics. 14(1): 1-17. Soma, P., Kotze, A., Grobler, J.P. and vanWyk, J.B. (2012). South African sheep breeds: population genetic structure and conservation implications. Small Ruminant Research. 103(2–3):112–119. Upadhyay, M., Bortoluzzi, C., Barbato, M., Ajmonemarsan, P., Colli, L., Ginja, C. et al. (2019). Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome‐wide SNPs. Evolutionary applications. 12(5): 951-963. Uzzaman, M.R., Zewdu Edea, M., Bhuiyan, S.A., Walker, J., Bhuiyan, A.K.F.H. and Kim, K. S. (2014). Genome-wide single nucleotide polymorphism analyses reveal genetic diversity and structure of wild and domestic cattle in Bangladesh. Asian-Australasian journal of animal sciences. 27(10): 1381. Weir, B.S., and Cockerham, C.C. (1984). Estimating F-statistics for the analysis of population structure. Evolution. 1358-1370. Wultsch, C., Waits, L.P. and Kelly, M.J. (2016). A comparative analysis of genetic diversity and structure in jaguars (Panthera onca), pumas (Puma concolor), and ocelots (Leopardus pardalis) in fragmented landscapes of a critical Mesoamerican linkage zone. PloS one. 11(3). Zeder, M.A., Emshwiller, E., Smith, B.D. and Bradley, D.G. (2006). Documenting domestication: the intersection of genetics and archaeology. TRENDS in Genetics. 22(3): 139-155. | ||
|
آمار تعداد مشاهده مقاله: 346 تعداد دریافت فایل اصل مقاله: 260 |
||