تعیین جایگاه‌های تحت انتخاب مثبت در نژادهای گوسفند ایرانی بلوچی و زل

نوع مقاله : مقاله پژوهشی

نویسندگان

1 دانشجوی کارشناسی ارشد، گروه علوم دامی، دانشکدۀ علوم و مهندسی کشاورزی، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج

2 دانشیار، گروه علوم دامی، دانشکدۀ علوم و مهندسی کشاورزی، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج

3 استادیار، دانشکدۀ کشاورزی و منابع طبیعی دانشگاه اراک

4 استادیار، دانشگاه علوم کشاورزی و منابع طبیعی ساری

چکیده

نشانه­های انتخاب در کل ژنگان (ژنوم)، ما را در درک سازوکار­های انتخاب و شناسایی مناطقی از ژنگان که در طی سالیان متمادی به‌صورت طبیعی و یا مصنوعی انتخاب شده­اند، راهنمایی می­کنند. هدف این تحقیق شناسایی نقاطی از ژنگان در گوسفندان زل و بلوچی بود که در طی سال­های مختلف به‌صورت مصنوعی یا طبیعی انتخاب شده­اند. 143 رأس گوسفند بلوچی (96 رأس) و زل (47 رأس)، با استفاده از آرایه­های ژنگانیIllumina ovine SNP50K BeadChip  تعیین ژنوتیپ شدند. برای جستجوی نشانه­های انتخاب از آزمون نااُریب FST ویر و کوکرهام (تتا) در بستۀ نرم‌افزاری R استفاده شد. نتایج 17 منطقۀ ژنگانی روی کروموزوم­های 3، 4، 5، 7، 10، 11، 12، 13، 15، 18 و X را شناسایی کرد. تجزیه‌وتحلیل‌ اطلاعات زیستی (بیوانفورماتیکی) نشان داد که برخی از این مناطق ژنگانی با ژن­های مؤثر بر صفات گسترش نظام استخوان‌بندی (اسکلتی) و دم، ایمنی و یاخته‌شناختی (سیتولوژی) یاخته‌ای، سوخت‌و‌ساز (متابولیسم) قند و انرژی و تولید­مثلی مانند ژن­های RPS6KA3، HOXB9، ESPL1، AAAS، FNDC3A همپوشانی دارند. نتایج این تحقیق و جایگاه­های ژنگانی شناسایی‌شده می­تواند نقش مهمی در رابطه با بررسی تأثیر انتخاب در تمایز جمعیتی دو نژاد دنبه‌دار بلوچی و بدون دنبۀ زل و در پی آن شناسایی مناطق ژنگانی مرتبط با صفات متمایزکنندۀ این دو نژاد داشته باشد.

کلیدواژه‌ها


عنوان مقاله [English]

Detection of loci under positive selection in Iranian Baluchi and Zel sheep breeds

نویسندگان [English]

  • Zeinab Manzari 1
  • Hassan Mehrabani Yeghaneh 2
  • Ardeshir Najati-Javaremi 2
  • Mohammad Hossein Moradi 3
  • Mohsen Gholizadeh 4
1 M. Sc. Student, Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
2 Associate Professor, Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
3 Assistant Professor, Department of Animal Science, College of Agriculture and Natural Resources, University of Arak, Iran
4 Assistant Professor, Department of Animal Science, Sari Agricultural Sciences and Natural Resources University, Iran
چکیده [English]

Selective signatures in whole genome can help us to understand the mechanisms of selection and to identify the genomic regions that have been under natural or artificial selection during long years. The objective of this study was to identify the genomic regions that have been under artificial and natural selection in Baluchi and Zel sheep breeds. 143 sheep from Baluchi (N=96) and Zel breeds (N=47) have been genotyped using the Illumina ovine SNP50 BeadChip. Unbiased method of Weir and Cockerham’s FST (Theta) was used to detect the selection signatures in the R package. The results revealed seventeen genomic regions on 3, 4, 5, 7, 10, 11, 12, 13, 15, 18 and X chromosomes. Bioinformatics analysis demonstrated that some of these genomic regions overlapped with reported genes included in the development of the skeletal system and tail, cytology cells, immune system, sugar and energy metabolism and reproduction traits such as RPS6KA3, HOXB9, ESPL1, AAAS, FNDC3A genes. The results of the present study and the identified genomic regions can play an important role in study of the effect of the selection on population differentiation in two Baluchi fat-tailed and Zel thin-tailed breeds and subsequently, would direct us to identify the genomic regions associated with traits differentiate these breeds.

کلیدواژه‌ها [English]

  • Baluchi sheep
  • candidate genes
  • Positive selection
  • unbiased method of Weir and Cockerham’s FST
  • Zel sheep
  1. Akey, J. M., Zhang, G., Zhang, K., Jin, L. & Shriver, M. D. (2002). Interrogating ahigh density SNP map for signatures of natural selection. Genome research, 12(12), 1805-14.
  2. Amaral, A. J., Ferretti, L., Megens, H. J., Crooijmans, R. P., Nie, H., Ramos-Onsins, S. E. & et al. (2011). Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA. PLoS One, 6(4), e14782.
  3. Aquadro, C. F., Bauer Dumont, V. & Reed, F. A. (2001). Genome-widevariation in the human and fruitfly: a comparison. Current Opinion in Genetics & Development, 11, 627-634.
  4. Barendse, W., Harrison, B. E., Bunch, R. J., Thomas, M. B. & Turner, L. B. (2009). Genome wide signatures of positive selection, the comparison of independent samples and the identification of regions associated to traits. BMC Genomics, 10, 178.
  5. Barreiro, L. B., Laval, G., Quach, H., Patin, E. & Quintana-Murci, L. (2008). Natural selection has driven population differentiation in modern humans. Nat Genet, 40, 340-345.
  6. Bonhomme, M., Chevalet, C., Servin, B., Boitard, S., Abdallah, J., Blott, S. & Sancristobal, M. (2010). Detecting selection in population trees: the Lewontin and Krakauer test extended. Genetics, 186, 241-62.
  7. Cavanagh, C. R., Attard, G., Palmer, D., Thomson, P. C., Tammen, I. & Raadsma, H. W. (2003). Comparisons of quantitative trait loci (QTL) detected for fat deposition in sheep using computed tomography. In: 15th Conference of the Association for the Advancement of Animal Breeding and Genetics, 7th-11th July., University of Melbourne,  Melbourne, pp. 367-370.
  8. Chen, F. & Capecchi, M. R. (1999). Paralogous mouse Hox genes, Hoxa9, Hoxb9, and Hoxd9, function together to control development of the mammary gland in response to pregnancy.PNAS, 96, 541-546.
  9. Chessa, B., Pereira, F., Arnaud, F., Amorim, A., Goyache, F., Mainland, I. & et al. (2009). Revealing the history of sheep domestication using retrovirus integrations. Science, 324, 532-536.
  10. Economides, K. D., Zeltser, L. & Capecchi, M. R. (2003). Hoxb13 mutations cause overgrowth of caudal spinal cord and tail vertebrae. Dev Biol, 256, 317-330.
  11. Ensembl BioMart: Ensembl online genome data base BioMart Tool. http:// www.ensembl.org/biomart/martview/.
  12. Fariello, M. I., Servin, B., Tosser-Klopp, G., Rupp, R., Moreno, C., San Critobal, M., Boitard, S. & Consortium, I. S. G. (2014). Selection Signatures in Worldwide Sheep Populations. PLoS ONE, 9(8), e103813.
  13. Fredriksson, R., Nordstrom, K. J., Stephansson, O., Hagglund, M. G. & Schioth, H. B. (2008). The solute carrier (SLC) complement of the human genome: phylogenetic classification reveals four major families. FEBS letters, 582, 3811-3816.
  14. Gely-Pernot, A., Raverdeau, M., Celebi, C., Dennefeld, C., Feret, B., Klopfenstein, M. & et al. (2012). Spermatogonia differentiation requires retinoic acid receptor gamma. Endocrinology, 153, 438-449.
  15. GeneCards. http://www.genecards.org/cgi-bin/carddisp.pl?gene=STAT
  16. Gholizadeh, M., Rahimi-Mianji, G., Nejati-Javaremi, A., De Koning, D. J. & Jonas, E. (2014). Genomewide association study to detect QTL for twinning rate in Baluchi sheep. Journal of Genetics, 93(2), 489-93.
  17. Hancock, A. M., Brachi, B., Faure, N., Horton, M. W., Jarymowycz, L. B., Sperone, F. G. & et al. (2011). Adaptation to climate across the Arabidopsis thaliana genome. Science, 334, 83-86.
  18. Helms, C. (1990). Salting out Procedure for Human DNA extraction. Retrieved April 20, 2010, from http://humgen.wustl.edu/hdk_lab_manual/dna/dna2.html.
  19. Kijas, J. W., Lenstra, J. A., Hayes, B., Boitard, S., Neto, L. R. P., San Cristobal, M. & et al. (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.
  20. Khaldari, M., Kashan, N.E.J., Afzalzadeh, A. & Salehi, A. (2007). Growth and carcass characteristics of crossbred progeny from lean tailed and fat tailed sheep breeds. South African Journal of Animal Science, 37(1), 51-56.
  21. Khaldari, M. (2014). Sheep and goat husbandry (5th Ed.). Jahade-daneshgahi publisher (in Farsi).
  22. Lim, C. H., Jeong, W., Lim, W., Kim, K., Song, G. & Bazer, F. W. (2012). Differential Expression of Select Members of the SLC Family of Genes and Regulation of Expression by MicroRNAs in the Chicken Oviduct. Biology of Reproduction, 87(6), 1-9.
  23. Lopez, M. E., Naira, R. & Yanez, J. M. (2015). Applications in the search for genomic selection signatures in fish. Frontiers in Genetics, 458(5), 1-12.
  24. Lv, F. H., Agha, S., Kantanen, J., Colli, L., Stucki, S. & Kijas, J. W. (2014). Adaptations to climate-mediated selective pressures in sheep. Molecular biology and evolution, 31(12), 3324-3343.
  25. Marai, I. F. M., Daader, A. H. & Bahgat, L. B. (2009). Performance traits of purebred Ossimi and Rahmani lambs and their crosses with Finnsheep born under two accelerated mating systems. Arch Tierz, 52, 497-51.
  26. MacEachern, S., Hayes, B., McEwan, J. & Goddard, M. (2009). An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle. BMC Genomics, 10, 181.
  27. Morgan, C. C., Loughran, N. B., Walsh, T. A., Harrison, A. J. & O’Connell, M. J. (2010).  Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins. BMC Evolutionary, 10, 39.
  28. Moradi, M. H., Nejati-Javaremi, A., Moradi-Shahrbabak, M., Dodds, K.G. & McEwan, J. C., (2012). Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition. BMC Genetics, 13, 10.
  29. Mottaghinia, Gh., Farhangfar, H. & Jafari, M. (2012). A study of inbreeding trend and its effect on wool weight of Baluchi sheep in Abbas Abad breeding center of Mashhad. Journal of Animal Science Researches, 22(2), 121-129. (in Farsi)
  30. Nielsen, R. (2005). Molecular signatures of natural selection. Annu. Rev. Genet, 39, 197-218.
  31. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D. & et al. (2007). PLINK: a toolset for whole-genome association and population-based linkage analysis. The American Journal of Human Genetics, 81, 559-575.
  32. Ramey, H., Decker, J., McKay, S., Rolf, M., Schnabel, R. & Taylor, J. (2013). Detection of selective sweeps in cattle using genome-wide SNP data. BMC Genomics, 14, 382.
  33. Randhawa, I. A. S., Khatkar, M. S., Thomson, P. C. & Raadsma, H. W. (2014). Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep. BMC Genetics, 15, 34.
  34. Saadat-Noori, M. & Siah-Mansoor, S. (1987). Sheep husbandry and management. Asharfi Pub. Co. Tehran, Iran. (in Farsi)
  35. Shrestha, B., Ansari, K. I., Bhan, A., Kasiri, S., Hussain, I. & Mandal, S. S. (2012). Homeodomain-containing protein HOXB9 regulates expression of growth and angiogenic factors, facilitates tumor growth in vitro and is overexpressed in breast cancer tissue. FEBS Journal, 279(19), 3715-3726
  36. Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D. & et al. (2014). STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic acids research, D447-452.
  37. Teo, Y. Y., Fry, A. E., Clark, T. G., Tai, E. S. & Seielstad, M. (2007). On the usage of HWE for identifying genotyping errors. Annals of Human Genetics, 71, 701-703.
  38. The R Project for Statistical Computing: Free software environment for statistical computing and graphics. http:// www.r-project.org/.
  39. Unal, N., Akcapinar, H., Aytac, M. & Atasoy, F. (2006).  Fattening performance and carcass traits in crossbred ram lambs. Medycyna Weterynaryjna, 62(2), 401-404.
  40. UniProtKB Gene. http://www.uniprot.org/help/gene_name.
  41. Van den Akker, E., Fromental-Ramain, C., de Graaff, W., Le Mouellic, H., Brulet, P., Chambon, P. & Deschamps, J. (2001). Axial skeletal patterning in mice lacking all paralogous group 8 Hox genes. Development, 128, 1911-1921.
  42. Vaysse, A., Ratnakumar, A., Derrien, T., Axelsson, E., Pielberg, G. R., Sigurdsson, S., Fall, T., Seppala, E. H., Hansen, M. S. & Lawley, C. T. (2011). Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS Genetics, 7(10), e1002316.
  43. Wang, H., Zhang, L., Cao, J., Wu, M., Ma, X., Liu, Z. & et al. (2015). Genome-Wide Specific Selection in Three Domestic Sheep Breeds. PLoS ONE, 10(6), e0128688.
  44. Weedon, M. N., Lango, H., Lindgren, C. M., Wallace, C., Evans, D. M., Mangino, M. & et al. (2008). Genome-wide association analysis identifies 20 loci that influence adult height. Nature genetics, 40(5), 575-83.
  45. Wei, C. H., Wang, H. H., Liu, G., Wu, M. M., Cao, J. X. V., Liu, Z. & et al. (2015). Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds. BMC Genomics, 16, 194.
  46. Weir, B. S. & Cockerham, C. C. (1984). Estimating F-Statistics for the analysis of population structure. Evolution, 38(6), 1358-1370.
  47. Zeder, M. A. (1999). Animal domestication in the Zagros: a review of past and current research. Pale´orient, 25, 11-26.
  48. Zheng, Y. H., Rengaraj, D., Choi, J. W., Park, K. J., Lee, S. I. & Han, J. Y. (2009). Expression pattern of meiosis associated SYCP family members during germline development in chickens. Reproduction, 138(3), 483-92.
  49. Zhu, C., Fan, H., Yuan, Z., Hu, S., Zhang, L., Wei, C. & et al. (2015). Detection of Selection Signatures on the X chromosome in Three Sheep Breeds. International Journal of Molecular Sciences, 6(9), 20360-20374.