8954856055505db

شناسایی نواحی تحت انتخاب مثبت در ژنگان اسب‌های کرد و عرب ایرانی با استفاده از روش مبتنی بر نامتعادلی پیوستگی ژنی

نوع مقاله: مقاله پژوهشی

نویسندگان

1 دانشجوی دکتری، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج

2 دانشیار، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج

3 استاد، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج

چکیده

اسب­های عرب به داشتن عملکرد خوب در مسابقه‌های استقامتی، پرش و زیبایی شهرت دارند. اسب­های کرد بومی منطقه‌های کوهستانی غرب ایران، مناسب مسابقه‌های چوگان هستند. اسب­های کرد، قد کوتاه­تر و وزن سنگین­تری نسبت به اسب­های عرب دارند. در این بررسی آمارۀ XP-EHH که مبتنی بر نامتعادلی پیوستگی ژنی (لینکاژی) است برای شناسایی قطعه‌های کروموزومی تحت انتخاب در ژنگان (ژنوم) اسب­های کرد و عرب ایرانی استفاده شد. برای این منظور، از نمونۀ خون و مو 38 اسب عرب و 58 اسب کرد DNA ژنگانی استخراج شد. همۀ نمونه­ها DNA توسط آرایۀ Axiom MNEC670 تعیین نژادگان (ژنوتیپ) شدند. پس از پالایش داده‌ها آمارۀ XP-EHH محاسبه شد. در اسب­های عرب 51 جایگاه (85 ژن) و در اسب‌های کرد 7 جایگاه (13 ژن) تحت انتخاب شناسایی شد. نواحی تحت انتخاب در اسب­های عرب با مسیرهای درگیر در سامانۀ ایمنی، تشکیل پروتئین شیر، رشد و نمو و سوخت‌وساز (متابولیسم) ماهیچه، بینایی، شبکۀ عصبی و اندازۀ بدن مرتبط بودند درحالی‌که در اسب­های کرد با مسیر گیرندۀ جفت‌شونده با پروتئین G، رشد و بلوغ فیبرهای ماهیچه، تنظیم خون بندآوری (هموستازی) اکسیژن یاخته‌ای، رنگدانه­سازی در پوست و مو ارتباط داشتند.

کلیدواژه‌ها


عنوان مقاله [English]

Identification of positive selection signatures in Iranian Kurdish and Arabian horses by linkage disequilibrium-based method

نویسندگان [English]

  • Saber Mohammad Maghsoodi 1
  • Hassan Mehrabani Yeganeh 2
  • Ardeshir Nejati Javaremi 3
1 Ph.D. Candidate, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran
2 Associate Professor, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran
3 Professor, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran
چکیده [English]

The Arab horses are famous for endurance riding, jumping and beauty. Kurdish horses are native to hilly regions of west of Iran and they are suitable for Polo tournament. Kurdish horses are shorter and heavier than Arabian horses. In this study, we use the linkage disequilibrium-based method, XP-EHH statistic, for Identification of regions that have undergone selection in the genome of Arabian and Kurdish horses. For this purpose, genomic DNA from blood and hair samples from 38 Arabian and 58 Kurdish horses were extracted. All DNA samples genotyped by the Axiom MNEC670 array. After data pruning, XP-EHH statistic was calculated. We identified 51 genomic regions (85 genes) in Iranian Arab horses and 7 genomic regions (13 genes) in Kurdish horses showing signatures of selection. We found positively selected genomic regions in the Iranian Arab horses associated with immune system related pathways, milk protein formation, muscle growth and development, vision, nervous system and body size whereas in the Kurdish horses associated with G protein–coupled receptors, growth and maturation of muscle fibers, cellular oxygen homeostasis and skin and hair pigmentation.

کلیدواژه‌ها [English]

  • Iranian Arab horse
  • Kurdish horse
  • selection signatures
  • XP-EHH
  1. Ala Amjadi, M., Mehrabani Yeganheh, H. & Sadeghi, M. (2018). A study of genetic diversity of Kurdish horse population in Iran using Micro-satellite indicators. In: Proceedings of 10th International Congress On Genetics Applied To Livestock Production, 11-16 Feb., Aotea Centre, Auckland, New Zealand, pp. 799.
  2. Areal, H., Abrantes, J. & Esteves, P. J. (2011). Signatures of positive selection in Toll-like receptor (TLR) genes in mammals. BMC Evolutionary Biology, 11, 368.
  3. Baysal, B. E., Lawrence, E. C. & Ferrell, R. E. (2007). Sequence variation in human succinate dehydrogenase genes: evidence for long-term balancing selection on SDHA. BMC Biology, 5, 12.
  4. Beltrán, N. A. R., Meira, C. T., de Oliveira, H. N., Pereira, G. L., Silva, J. A. I. I. V., da Mota, M. D. S. & Curi, R. A. (2015). Prospection of genomic regions divergently selected in cutting line of Quarter Horses in relation to racing line. Livestock Science, 174 (Supplement C), 1-9.
  5. Bimonte, S., De Angelis, A., Quagliata, L., Giusti, F., Tammaro, R., Dallai, R., Ascenzi, M.-G., Diez-Roux, G. & Franco, B. (2011). Ofd1 is required in limb bud patterning and endochondral bone development. Developmental Biology, 349(2), 179-191.
  6. Brinkmann, J., Jagannathan, V., Drogemuller, C., Rieder, S., Leeb, T., Thaller, G. & Tetens, J. (2016). Genetic variability of the equine casein genes. Journal of Dairy Science, 99(7), 5486-5497.
  7. Capomaccio, S., Cappelli, K., Barrey, E., Felicetti, M., Silvestrelli, M. & Verini-Supplizi, A. (2010). Microarray analysis after strenuous exercise in peripheral blood mononuclear cells of endurance horses. Animal Genetics, 41 Suppl 2, 166-175.
  8. Chang, T. C., Klabnik, J. L. & Liu, W. S. (2011). Regional selection acting on the OFD1 gene family. PLoS One, 6(10), e26195.
  9. Chen, H., Patterson, N. & Reich, D. (2010). Population differentiation as a test for selective sweeps. Genome Research, 20(3), 393-402.
  10. Chen, M., Pan, D., Ren, H., Fu, J., Li, J., Su, G., Wang, A., Jiang, L., Zhang, Q. & Liu, J. F. (2016). Identification of selective sweeps reveals divergent selection between Chinese Holstein and Simmental cattle populations. Genetics Selection Evolution, 48(1), 76.
  11. Clarkson, P. M. & Sayers, S. P. (1999). Etiology of exercise-induced muscle damage. Canadian Journal of Applied Physiology, 24(3), 234-248.
  12. Cole, J. B., Wiggans, G. R., Ma, L., Sonstegard, T. S., Lawlor, T. J., Jr., Crooker, B. A., Van Tassell, C. P., Yang, J., Wang, S., Matukumalli, L. K. & Da, Y. (2011). Genome-wide association analysis of thirty-one productions, health, reproduction and body conformation traits in contemporary U.S. Holstein cows. BMC Genomics, 12, 408.
  13. Conley, Y. P., Jakobsdottir, J., Mah, T., Weeks, D. E., Klein, R., Kuller, L., Ferrell, R. E. & Gorin, M. B. (2006). CFH, ELOVL4, PLEKHA1 and LOC387715 genes and susceptibility to age-related maculopathy: AREDS and CHS cohorts and meta-analyses. Human Molecular Genetics, 15(21), 3206-3218.
  14. Daub, J. T., Hofer, T., Cutivet, E., Dupanloup, I., Quintana-Murci, L., Robinson-Rechavi, M. & Excoffier, L. (2013). Evidence for polygenic adaptation to pathogens in the human genome. Molecular Biology and Evolution, 30(7), 1544-1558.
  15. Dennis, G., Jr., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C. & Lempicki, R. A. (2003). DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biology, 4(5), P3.
  16. Diamond, J. (2002). Evolution, consequences and future of plant and animal domestication. Nature, 418(6898), 700-707.
  17. Emond, M. R., Biswas, S. & Jontes, J. D. (2009). Protocadherin-19 is essential for early steps in brain morphogenesis. Developmental Biology, 334(1), 72-83.
  18. Gautier, M. & Vitalis, R. (2012). rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics, 28(8), 1176-1177.
  19. Gharahveysi, S. & Irani, M. (2011). Inbreeding Study on the Iranian Arab Horse Population. World Journal of Zoology, 6(1), 1-6.
  20. Gu, J., Orr, N., Park, S. D., Katz, L. M., Sulimova, G., MacHugh, D. E. & Hill, E. W. (2009). A genome scan for positive selection in thoroughbred horses. PLoS One, 4(6), e5767.
  21. Guttridge, D. C. (2011). Making muscles grow by g protein-coupled receptor signaling. Sci Signal, 4(201), pe45.
  22. Hayes, B. J., Chamberlain, A. J., Maceachern, S., Savin, K., McPartlan, H., MacLeod, I., Sethuraman, L. & Goddard, M. E. (2009). A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle. Animal Genetics, 40(2), 176-184.
  23. Hensen, E. F. & Bayley, J. P. (2011). Recent advances in the genetics of SDH-related paraganglioma and pheochromocytoma. Familial Cancer, 10(2), 355-363.
  24. Her, Y. F., Nelson-Holte, M. & Maher, L. J., 3rd. (2015). Oxygen concentration controls epigenetic effects in models of familial paraganglioma. PLoS One, 10(5), e0127471.
  25. Hider, J. L., Gittelman, R. M., Shah, T., Edwards, M., Rosenbloom, A., Akey, J. M. & Parra, E. J. (2013). Exploring signatures of positive selection in pigmentation candidate genes in populations of East Asian ancestry. BMC Evolutionary Biology, 13, 150.
  26. Kader, A., Li, Y., Dong, K., Irwin, D. M., Zhao, Q., He, X., Liu, J., Pu, Y., Gorkhali, N. A., Liu, X., Jiang, L., Li, X., Guan, W., Zhang, Y., Wu, D. D. & Ma, Y. (2016). Population Variation Reveals Independent Selection toward Small Body Size in Chinese Debao Pony. Genome Biology and Evolution, 8(1), 42-50.
  27. Kang, H. Y., Lee, B., Lee, D. O., Kim, K., Jung, J. M., Ahn, C. & Jeung, E.-B. (2016). Equine Tight Junctions: Tissue-Specific Localization and Expression of Junction Adhesion Molecule-A, Zona Occludens-1, and Occludin. Journal of Equine Veterinary Science, 46, 7-14.
  28. Kim, H., Lee, T., Park, W., Lee, J. W., Kim, J., Lee, B. Y., Ahn, H., Moon, S., Cho, S., Do, K. T., Kim, H. S., Lee, H. K., Lee, C. K., Kong, H. S., Yang, Y. M., Park, J., Kim, H. M., Kim, B. C., Hwang, S., Bhak, J., Burt, D., Park, K. D., Cho, B. W. & Kim, H. (2013). Peeling back the evolutionary layers of molecular mechanisms responsive to exercise-stress in the skeletal muscle of the racing horse. DNA Research, 20(3), 287-298.
  29. Kimura, R., Fujimoto, A., Tokunaga, K. & Ohashi, J. (2007). A practical genome scan for population-specific strong selective sweeps that have reached fixation. PLoS One, 2(3), e286.
  30. Klein, C. & Troedsson, M. H. (2011). Transcriptional profiling of equine conceptuses reveals new aspects of embryo-maternal communication in the horse. Biology of Reproduction, 84(5), 872-885.
  31. Lester, S. N. & Li, K. (2014). Toll-like receptors in antiviral innate immunity. Journal of Molecular Biology, 426(6), 1246-1264.
  32. Liu, Q., Chen, Y., Kubota, F., Pan, J. J. & Murakami, T. (2010). Expression of protocadherin-19 in the nervous system of the embryonic zebrafish. International Journal of Developmental Biology, 54(5), 905-911.
  33. Liu, X. X., Pan, J. F., Zhao, Q. J., He, X. H., Pu, Y. B., Han, J. L., Ma, Y. H. & Jiang, L. (2018). Detecting selection signatures on the X chromosome of the Chinese Debao pony. Journal of Animal Breeding and Genetics, 135(1), 84-92.
  34. Ma, Y., Zhang, H., Zhang, Q. & Ding, X. (2014). Identification of selection footprints on the X chromosome in pig. PLoS One, 9(4), e94911.
  35. Maghsoodi, S. M., Mehrabani Yeganheh, H., Nejati Javaremi, A. & Yousefi Mashouf, N. (2017). Investigating population structure and identifying signatures of selection in Iranian Kurdish and Arabian horses. Iranian Journal of Animal Science, 48(3), 429-438. (in Farsi)
  36. Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., Shafer, A., Neri, F., Lee, K., Kutyavin, T., Stehling-Sun, S., Johnson, A. K., Canfield, T. K., Giste, E., Diegel, M., Bates, D., Hansen, R. S., Neph, S., Sabo, P. J., Heimfeld, S., Raubitschek, A., Ziegler, S., Cotsapas, C., Sotoodehnia, N., Glass, I., Sunyaev, S. R., Kaul, R. & Stamatoyannopoulos, J. A. (2012). Systematic localization of common disease-associated variation in regulatory DNA. Science, 337(6099), 1190-1195.
  37. McGowan, K. A., Li, J. Z., Park, C. Y., Beaudry, V., Tabor, H. K., Sabnis, A. J., Zhang, W., Fuchs, H., de Angelis, M. H., Myers, R. M., Attardi, L. D. & Barsh, G. S. (2008). Ribosomal mutations cause p53-mediated dark skin and pleiotropic effects. Nature Genetics, 40(8), 963-970.
  38. Metzger, J., Karwath, M., Tonda, R., Beltran, S., Agueda, L., Gut, M., Gut, I. G. & Distl, O. (2015). Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses. BMC Genomics, 16, 764.
  39. Mi, H., Muruganujan, A. & Thomas, P. D. (2013). PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Research, 41(Database issue), D377-386.
  40. Mienaltowski, M. J., Huang, L., Stromberg, A. J. & MacLeod, J. N. (2008). Differential gene expression associated with postnatal equine articular cartilage maturation. BMC Musculoskelet Disord, 9, 149.
  41. Montague, M. J., Li, G., Gandolfi, B., Khan, R., Aken, B. L., Searle, S. M., Minx, P., Hillier, L. W., Koboldt, D. C., Davis, B. W., Driscoll, C. A., Barr, C. S., Blackistone, K., Quilez, J., Lorente-Galdos, B., Marques-Bonet, T., Alkan, C., Thomas, G. W., Hahn, M. W., Menotti-Raymond, M., O'Brien, S. J., Wilson, R. K., Lyons, L. A., Murphy, W. J. & Warren, W. C. (2014). Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proc Natl Acad Sci USA, 111(48), 17230-17235.
  42. Moridi, M., Masoudi, A. A., Vaez Torshizi, R. & Hill, E. W. (2013). Mitochondrial DNA D-loop sequence variation in maternal lineages of Iranian native horses. Anim Genet, 44(2), 209-213.
  43. Mosapour Kaleibar, P., Aghazade, A. M., Hassanpour, A., Mahpeikar, H. A. & Ebrahimi Hamed, M. (2007). A study on some phenotypic characteristics of the Karabakh horse in comparison with the Kurdish and Arabian horses. J. Spe Vet Sci Islam Azad Uni Tabriz, 1(1), 27-33. (in Farsi)
  44. Oleksyk, T. K., Smith, M. W. & O'Brien, S. J. (2010). Genome-wide scans for footprints of natural selection. Philosophical Transactions of the Royal Society of London B: Biological Sciences, 365(1537), 185-205.
  45. Petersen, J. L., Mickelson, J. R., Rendahl, A. K., Valberg, S. J., Andersson, L. S., Axelsson, J., Bailey, E., Bannasch, D., Binns, M. M., Borges, A. S., Brama, P., da Camara Machado, A., Capomaccio, S., Cappelli, K., Cothran, E. G., Distl, O., Fox-Clipsham, L., Graves, K. T., Guerin, G., Haase, B., Hasegawa, T., Hemmann, K., Hill, E. W., Leeb, T., Lindgren, G., Lohi, H., Lopes, M. S., McGivney, B. A., Mikko, S., Orr, N., Penedo, M. C., Piercy, R. J., Raekallio, M., Rieder, S., Roed, K. H., Swinburne, J., Tozaki, T., Vaudin, M., Wade, C. M. & McCue, M. E. (2013). Genome-wide analysis reveals selection for important traits in domestic horse breeds. PLoS Genet, 9(1), e1003211.
  46. Pickrell, J. K., Coop, G., Novembre, J., Kudaravalli, S., Li, J. Z., Absher, D., Srinivasan, B. S., Barsh, G. S., Myers, R. M., Feldman, M. W. & Pritchard, J. K. (2009). Signals of recent positive selection in a worldwide sample of human populations. Genome Research, 19(5), 826-837.
  47. Ponsuksili, S., Murani, E., Phatsara, C., Schwerin, M., Schellander, K. & Wimmers, K. (2009). Porcine muscle sensory attributes associate with major changes in gene networks involving CAPZB, ANKRD1, and CTBP2. Funct Integr Genomics, 9(4), 455-471.
  48. Qanbari, S., Strom, T. M., Haberer, G., Weigend, S., Gheyas, A. A., Turner, F., Burt, D. W., Preisinger, R., Gianola, D. & Simianer, H. (2012). A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens. PLoS One, 7(11), e49525.
  49. Rafeie, F., Amirinia, C., Nejati Javaremi, A., Mirhoseini, S. Z. & Amirmozafari, N. (2011). A study of patrilineal genetic diversity in Iranian indigenous horse breeds. African Journal of Biotechnology, 10(75), 17347-17352.
  50. Roll, P., Rudolf, G., Pereira, S., Royer, B., Scheffer, I. E., Massacrier, A., Valenti, M. P., Roeckel-Trevisiol, N., Jamali, S., Beclin, C., Seegmuller, C., Metz-Lutz, M. N., Lemainque, A., Delepine, M., Caloustian, C., de Saint Martin, A., Bruneau, N., Depetris, D., Mattei, M. G., Flori, E., Robaglia-Schlupp, A., Levy, N., Neubauer, B. A., Ravid, R., Marescaux, C., Berkovic, S. F., Hirsch, E., Lathrop, M., Cau, P. & Szepetowski, P. (2006). SRPX2 mutations in disorders of language cortex and cognition. Human Molecular Genetics, 15(7), 1195-1207.
  51. Rothammer, S., Seichter, D., Forster, M. & Medugorac, I. (2013). A genome-wide scan for signatures of differential artificial selection in ten cattle breeds. BMC Genomics, 14, 908.
  52. Sabeti, P. C., Schaffner, S. F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., Palma, A., Mikkelsen, T. S., Altshuler, D. & Lander, E. S. (2006). Positive natural selection in the human lineage. Science, 312(5780), 1614-1620.
  53. Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E. H., McCarroll, S. A., Gaudet, R., Schaffner, S. F., Lander, E. S., International HapMap, C., Frazer, K. A., Ballinger, D. G., Cox, D. R., Hinds, D. A., Stuve, L. L., Gibbs, R. A., Belmont, J. W., Boudreau, A., Hardenbol, P., Leal, S. M., Pasternak, S., Wheeler, D. A., Willis, T. D., Yu, F., Yang, H., Zeng, C., Gao, Y., Hu, H., Hu, W., Li, C., Lin, W., Liu, S., Pan, H., Tang, X., Wang, J., Wang, W., Yu, J., Zhang, B., Zhang, Q., Zhao, H., Zhao, H., Zhou, J., Gabriel, S. B., Barry, R., Blumenstiel, B., Camargo, A., Defelice, M., Faggart, M., Goyette, M., Gupta, S., Moore, J., Nguyen, H., Onofrio, R. C., Parkin, M., Roy, J., Stahl, E., Winchester, E., Ziaugra, L., Altshuler, D., Shen, Y., Yao, Z., Huang, W., Chu, X., He, Y., Jin, L., Liu, Y., Shen, Y., Sun, W., Wang, H., Wang, Y., Wang, Y., Xiong, X., Xu, L., Waye, M. M., Tsui, S. K., Xue, H., Wong, J. T., Galver, L. M., Fan, J. B., Gunderson, K., Murray, S. S., Oliphant, A. R., Chee, M. S., Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Olivier, J. F., Phillips, M. S., Roumy, S., Sallee, C., Verner, A., Hudson, T. J., Kwok, P. Y., Cai, D., Koboldt, D. C., Miller, R. D., Pawlikowska, L., Taillon-Miller, P., Xiao, M., Tsui, L. C., Mak, W., Song, Y. Q., Tam, P. K., Nakamura, Y., Kawaguchi, T., Kitamoto, T., Morizono, T., Nagashima, A., Ohnishi, Y., Sekine, A., Tanaka, T., Tsunoda, T., Deloukas, P., Bird, C. P., Delgado, M., Dermitzakis, E. T., Gwilliam, R., Hunt, S., Morrison, J., Powell, D., Stranger, B. E., Whittaker, P., Bentley, D. R., Daly, M. J., de Bakker, P. I., Barrett, J., Chretien, Y. R., Maller, J., McCarroll, S., Patterson, N., Pe'er, I., Price, A., Purcell, S., Richter, D. J., Sabeti, P., Saxena, R., Schaffner, S. F., Sham, P. C., Varilly, P., Altshuler, D., Stein, L. D., Krishnan, L., Smith, A. V., Tello-Ruiz, M. K., Thorisson, G. A., Chakravarti, A., Chen, P. E., Cutler, D. J., Kashuk, C. S., Lin, S., Abecasis, G. R., Guan, W., Li, Y., Munro, H. M., Qin, Z. S., Thomas, D. J., McVean, G., Auton, A., Bottolo, L., Cardin, N., Eyheramendy, S., Freeman, C., Marchini, J., Myers, S., Spencer, C., Stephens, M., Donnelly, P., Cardon, L. R., Clarke, G., Evans, D. M., Morris, A. P., Weir, B. S., Tsunoda, T., Johnson, T. A., Mullikin, J. C., Sherry, S. T., Feolo, M., Skol, A., Zhang, H., Zeng, C., Zhao, H., Matsuda, I., Fukushima, Y., Macer, D. R., Suda, E., Rotimi, C. N., Adebamowo, C. A., Ajayi, I., Aniagwu, T., Marshall, P. A., Nkwodimmah, C., Royal, C. D., Leppert, M. F., Dixon, M., Peiffer, A., Qiu, R., Kent, A., Kato, K., Niikawa, N., Adewole, I. F., Knoppers, B. M., Foster, M. W., Clayton, E. W., Watkin, J., Gibbs, R. A., Belmont, J. W., Muzny, D., Nazareth, L., Sodergren, E., Weinstock, G. M., Wheeler, D. A., Yakub, I., Gabriel, S. B., Onofrio, R. C., Richter, D. J., Ziaugra, L., Birren, B. W., Daly, M. J., Altshuler, D., Wilson, R. K., Fulton, L. L., Rogers, J., Burton, J., Carter, N. P., Clee, C. M., Griffiths, M., Jones, M. C., McLay, K., Plumb, R. W., Ross, M. T., Sims, S. K., Willey, D. L., Chen, Z., Han, H., Kang, L., Godbout, M., Wallenburg, J. C., L'Archeveque, P., Bellemare, G., Saeki, K., Wang, H., An, D., Fu, H., Li, Q., Wang, Z., Wang, R., Holden, A. L., Brooks, L. D., McEwen, J. E., Guyer, M. S., Wang, V. O., Peterson, J. L., Shi, M., Spiegel, J., Sung, L. M., Zacharia, L. F., Collins, F. S., Kennedy, K., Jamieson, R. & Stewart, J. (2007). Genome-wide detection and characterization of positive selection in human populations. Nature, 449(7164), 913-918.
  54. Scheet, P. & Stephens, M. (2006). A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. The American Journal of Human Genetics, 78(4), 629-644.
  55. Sokol, C. L. & Luster, A. D. (2015). The chemokine system in innate immunity. Cold Spring Harbor Perspectives in Biology, 7(5), a016303.
  56. Taye, M., Kim, J., Yoon, S. H., Lee, W., Hanotte, O., Dessie, T., Kemp, S., Mwai, O. A., Caetano-Anolles, K., Cho, S., Oh, S. J., Lee, H. K. & Kim, H. (2017a). Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef. BMC Genet, 18(1), 11.
  57. Taye, M., Lee, W., Jeon, S., Yoon, J., Dessie, T., Hanotte, O., Mwai, O. A., Kemp, S., Cho, S., Oh, S. J., Lee, H. K. & Kim, H. (2017b). Exploring evidence of positive selection signatures in cattle breeds selected for different traits. Mamm Genome, 28(11-12), 528-541.
  58. Taye, M., Yoon, J., Dessie, T., Cho, S., Oh, S. J., Lee, H.-K. & Kim, H. (2018). Deciphering signature of selection affecting beef quality traits in Angus cattle. Genes & Genomics, 40(1), 63-75.
  59. Uniacke-Lowe, T., Huppertz, T. & Fox, P. F. (2010). Equine milk proteins: Chemistry, structure and nutritional significance. International Dairy Journal, 20(9), 609-629.
  60. Utsunomiya, Y. T., Perez O'Brien, A. M., Sonstegard, T. S., Solkner, J. & Garcia, J. F. (2015). Genomic data as the "hitchhiker's guide" to cattle adaptation: tracking the milestones of past selection in the bovine genome. Frontiers in genetics, 6, 36.
  61. Utsunomiya, Y. T., Perez O'Brien, A. M., Sonstegard, T. S., Van Tassell, C. P., do Carmo, A. S., Meszaros, G., Solkner, J. & Garcia, J. F. (2013). Detecting loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods. PLoS One, 8(5), e64280.
  62. Vafaei Sayah, G. & Mehrannezhad, R. (2005). Cytogenetical study of Kurd horse. Pajouhesh & Sazandegi, 66, 75-79. (in Farsi)
  63. Vernot, B., Stergachis, A. B., Maurano, M. T., Vierstra, J., Neph, S., Thurman, R. E., Stamatoyannopoulos, J. A. & Akey, J. M. (2012). Personal and population genomics of human regulatory variation. Genome Res, 22(9), 1689-1697.
  64. Wu, H., Zhao, S. & Fan, B. (2010). Investigation of effects of the MKK3 and MKK6 genes on meat production traits in the pig (Brief Report). Archiv Tierzucht, 53(2), 242-245.
  65. Yousefi Mashouf, N. (2016). Phenotypic and genetic characterization of the Iranian Kurdish horse. Master of Science Thesis, College of Agriculture & Natural Resources, University of Tehran, Iran.
  66. Yu, W., Dong, S., Zhao, C., Wang, H., Dai, F. & Yang, J. (2013). Cumulative association between age-related macular degeneration and less studied genetic variants in PLEKHA1/ARMS2/HTRA1: a meta and gene-cluster analysis. Molecular Biology Reports, 40(10), 5551-5561.
  67. Zandi, A., Nejati-Javaremi, A. & Pakdel, A. (2014). Detecting selective sweeps using Equine 70k SNP array in two native Iranian horse breeds. In: Proceedings of the 34th International Society for Animal Genetics Conference, 27-1 Aug., Xi'an, China.
  68. Zhu, C., Fan, H., Yuan, Z., Hu, S., Zhang, L., Wei, C., Zhang, Q., Zhao, F. & Du, L. (2015). Detection of Selection Signatures on the X Chromosome in Three Sheep Breeds. International Journal of Molecular Sciences, 16(9), 20360-20374.