پویش ژنگان کل برای تعیین جایگاه‌های تحت انتخاب مثبت در گوسفندان نژاد زندی

نوع مقاله : مقاله پژوهشی

نویسندگان

1 دانشجوی دکتری گروه علوم دامی، دانشکدۀ کشاورزی، دانشگاه تبریز

2 استاد گروه علوم دامی، دانشکدۀ کشاورزی، دانشگاه تبریز

3 استادیار گروه علوم دامی، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج

4 گروه علوم دامی، دانشکده کشاورزی، دانشگاه تبریز.

5 استادیار گروه علوم دامی، دانشکدۀ کشاورزی و منابع طبیعی، دانشگاه اراک

چکیده

شناسایی مناطق ژنگانی (ژنوم) که هدف انتخاب بوده­اند، یکی از راهکار‌های اصلی تحقیقات زیستی است. هدف این پژوهش، پویش کل ژنگان برای شناسایی مناطقی از ژنگان گوسفندان نژاد زندی که در طی سال­های مختلف هدف انتخاب­های طبیعی یا مصنوعی قرار گرفته‌اند، بود. بدین منظور 96 رأس گوسفند نژاد زندی با استفاده از آرایه­های ژنگانی Illumina ovine SNP50K BeadChip تعیین ژنوتیپ شدند. برای شناسایی نشانه­های انتخاب بر پایۀ روش­های نداشتن تعادل پیوستگی (لینکاژی) از آزمون (iHS)integrated haplotype score استفاده شد. نتایج یازده منطقۀ ژنگانی روی کروموزوم­های 1 (2 منطقه)، 3، 6، 7، 8، 9، 10، 17، 22 و 26 را شناسایی کرد. تجزیه‌وتحلیل داده‌های زیستی (بیوانفورماتیکی) نشان داد، برخی از این مناطق ژنگانی به‌طور مستقیم و غیرمستقیم با ژن­های مؤثر بر سازگاری (آداپتاسیون) به آب‌وهوای گرم و خشک (DNAJB4، ­HSPA4L، MSRB3­)، پاسخ ایمنی (IL23A، STAT6، LY96)، توسعه و اندازۀ بدن (STAC3، LAP3)، توسعۀ نظام ساختار بدنی یا اسکلتی (SPP1، MEPE، IBSP) و سوخت‌وساز (متابولیسم) انرژی (ATP5B، GLS2، CS) همپوشانی دارند. درنهایت بررسیQTLهای گزارش‌شده در ژنگان گوسفند نشان داد، این مناطق با QTLهای صفات مهم اقتصادی از جمله صفات مرتبط با رشد، لاشه و پشم در ارتباط است. به‌هرحال، برای شناسایی دقیق این ژن­ها و QTLها لازم است بررسی‌های پیوستگی و عملکردی بیشتری انجام شود.

کلیدواژه‌ها

عنوان مقاله [English]

Genome-wide analysis for detection of loci under positive selection in Zandi sheep breed

نویسندگان [English]

  • Hossein Mohammadi 1
  • Seyed Abbas Rafat 2
  • Hossein Moradi Shahrbabak 3
  • Jalil Shoja 4
  • mohammad hosein moradi 5
1 Ph.D. Candidate, Department of Animal Science, Faculty of Agricultural Sciences, University of Tabriz, Iran
2 Professor, Department of Animal Science, Faculty of Agricultural Sciences, University of Tabriz, Iran
3 Assistant Professor, Department of Animal Sciences, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
4 Department of Animal Science, Faculty of Agricultural Sciences, University of Tabriz.
5 Assistant Professor, Department of Animal Sciences, Faculty of Agriculture and Natural Resources, University of Arak, Iran
چکیده [English]

Identification of selection targeted genomic regions is one of the main aims of biological research.The objective of this study was a genome-wide scan to identify the genomic regions that have been under artificial and natural selection in Zandi sheep breed. For this purpose, 96 animal of Zandi breed have been genotyped using the Illumina ovine SNP50 BeadChip. The intergrated hapl-type score (iHS) test was used to detect the selection sweep, due to linkage disequilibrium, associated with these signatures. The results revealed eleven genomic regions on 1 (two areas), 3, 6, 7,8, 9, 10, 17, 22 and 26 chromosomes. Bioinformatics analysis demonstrated that some of these genomic regions overlapped with reported genes that directly and indirectly influenced traits for adaptation to hot arid environments (DNAJB4, HSPA4L, MSRB3), immune response (IL23A, STAT6, LY96), body size and development (STAC3, LAP3), development of the skeletal system (SPP1, MEPE, IBSP) and energy and digestive metabolism (ATP5B, GLS2, CS). Finally, study of the reported QTL in these regions of the sheep genome showed that they overlapped with QTL of economically important traits such as carcass yield, growth and wool traits. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes.

کلیدواژه‌ها [English]

  • Adaptation
  • genome scan
  • iHS test
  • selection signature detection

مراجع

  1. Bahbahani, H. (2015). Genome-wide identification of signatures of positive selection in African admixed zebu cattle. Ph.D. thesis, University of Nottingham.
  2. Barrett, J. C., Fry, B., Maller, J. & Daly, M. J. (2005). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21(2), 263-265.
  3. Binelli, M., Scolari, S. C., Pugliesi, G., Van Hoeck, V., Gonella-Diaza, A. M. & Andrade, S. C. S. (2015). The Transcriptome Signature of the Receptive Bovine Uterus Determined at Early Gestation. PLoS ONE 10(4): e0122874. doi:10.1371/journal.pone.0122874.
  4. Bouleftour, W., Boudiffa, M., Wade-Gueye, N. M., Bouet, G., Cardelli, M., Laroche, N., et al. (2014). Skeletal development of mice lacking bone sialoprotein (BSP) Impairment of long bone growth and progressive establishment of high trabecular bone mass. PLoS ONE, 9:e95144.
  5. Codoner-Franch, P., Tavarez-Alonso, S., Murria-Estal, R., Herrera-Martin, G. & Alonso-Iglesias, E. (2011). Polyamines Are Increased in Obese Children and Are Related to Markers of Oxidative/Nitrosative Stress and Angiogenesis. The Journal of Clinical Endocrinology & Metabolism, 96, 2821-2825.
  6. Dalrymple, B. P., Kirkness, E. F., Nefedov, M., McWilliam, S., Ratnakumar, A., Barris, W., Zhao, S., Shetty, J., Maddox, J. F., O'Grady, M., et al.  (2007). Using comparative genomics to reorder the human genome sequence into a virtual sheep genome. Genome Biology, 8(7), R152.
  7. DeAtley, K. L., Rincon, G., Farber, C. R., Medrano, J. F., Luna-Nevarez, P., Enns, R. M., VanLeeuwen, D. M., Silver, G. A. & Thomas, M. G. (2011). Genetic analyses involving microsatellite ETH10 genotypes on bovine chromosome 5 and performance trait measures in Angus- and Brahman-influenced cattle. Journal of Animal Science, 89, 2031-2041.
  8. Denninger, K. C., Litman, T., Marstrand, T., Moller, K., Svensson, L., Labuda, T., et al. (2015). Kinetics of gene expression and bone remodelling in the clinical phase of collagen induced arthritis. Arthritis Research & Therapy, 17, 43.
  9. Ensembl BioMart:  Ensembl online genome data base BioMart Tool.  http://www.ensembl.org/biomart/martview/.
  10. Fariello, M. I., Servin, B., Tosser-Klopp, G., Rupp, R., Moreno, C., International Sheep Genomics Consortium. & et al. (2014). Selection Signatures in Worldwide Sheep Populations. PLoS ONE, 9(8), e103813.
  11. Fay, J. C. & Wu, C. I. (2000). Hitchhiking under positive Darwinian selection. Genetics, 155, 1405-1413.
  12. Gautier, M. & Naves, M. (2011). Footprints of selection in the ancestral admixture of a New World Creole cattle breed. Molecular Ecology, 20, 3128-3143.
  13. GeneCards. http://www.genecards.org/cgi-bin/carddisp.pl?gene=STAT
  14. Gossnera, A. G., Venturina, V. M., Peers, A., Watkinsb, C. A. & Hopkins, J. (2012). Expression  of  sheep  interleukin  23  (IL23A,  alpha  subunit  p19)  in  two distinct gastrointestinal diseases. Veterinary Immunology and Immunopathology, 150, 118-122.
  15. Gouveia, J. J. D. S., Paiva, S. R., McManus, C. M., Caetano, A. R., Kijas, J. W., Facó, O., Azevedo, H. C., Araujoi, A. M. D., Souza, C. J. H., Yamagishi, M. E. B., Carneiro, P. L. S., Lôbo, R. N. B., Oliveira, S. M. P. & da Silva, M. V. G. B. (2017). Genome-wide search for signatures of selection in three major Brazilian locally adapted sheep breeds. Livestock Science, 197, 36-45.
  16. Guðmundsdóttir, O. O. (2015). Genome-wide association study of muscle traits in Icelandic sheep. M.Sc. thesis. Agricultural University of Iceland.
  17. Gurgul, A., Szmatoła, T., Ropka-Molik, K., Jasielczuk, I., Pawlina, K., Semik, E. & Bugno-Poniewierska, M. (2015). Identification of genome-wide selection signatures in the Limousin beef cattle breed. Journal of Animal & Breeding Genetics, 1-13.
  18. 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.
  19. Huang, D. W., Sherman, B. T. & Lempicki, R. A. (2009). Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protocol, 4(1), 44-57. 
  20. Isabelle, C. M. & Picard, B. (2016). Expression Marker-Based Strategy to Improve Beef Quality. The Scientific World Journal, 1-11. Doi: 2185323.
  21. Khare, S., Lawhon, S. D., Drake, K. L., Nunes, J. E. S., Figueiredo, J. F., Rossetti, C. A., Gull, T., Everts, R. E., Lewin, H. A., Galindo, C. L., Garner, H. R. & Adams, L. G. (2012). Systems Biology Analysis of Gene Expression during In Vivo Mycobacterium avium paratuberculosis Enteric Colonization Reveals Role for Immune Tolerance. PLoS ONE, 7(8): e42127. doi:10.1371/journal.pone.0042127.
  22. Kim, E-S., Elbeltagy, A. R., Aboul-Naga, A. M., Rischkowsky, B., Sayre, B., Mwacharo, J. M. & Rothschild, M. F. (2015). Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment. Heredity, 1-10.
  23. Kijas,  J. W.,   Johannes, A.,  Ben  Hayes,  L.,  Boitard,  S.,  PortoNeto, L. R., Cristobal, M. S., Servin, B., McCulloch, R., Whan, V., Gietzen,  K.,  Paiva,  S.,  Barendse,  W.,  Ciani,  E.,  Raadsma,  H.,  McEwan, J. & Dalrymple, B. (2012). Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biology, 10, 1-14.
  24. Kong, R. S. G., Liang, G., Chen, Y., Stothard, P. & Guan, L. L. (2016). Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake. BMC Genomics, 17, 592.
  25. Lammers, G., Gilissen, C., Nillesen, S. T., Uijtdewilligen, P. J., Wismans, R. G., Veltman, J. A., Daamen, W. F. & van Kuppevelt, T. H. (2010). High density gene expression microarrays  and  gene  ontology  analysis  for  identifying  processes  in  implanted  tissue engineering constructs. Biomaterials, 31(32), 8299-8312.
  26. Luna-Nevarez, P., Rincon, G., Medrano, J. F., Riley, D. G., Chase Jr., C. C., Coleman, S. W., VanLeeuwen, D. M., DeAtley, K. L., Islas-Trejo, A., Silver, G. A. & Thomas, M. G. (2011). Single nucleotide polymorphisms in the growth hormone–insulin-like growth factor axis in straightbred and crossbred Angus, Brahman, and Romosinuano heifers: Population genetic analyses and association of genotypes with reproductive phenotypes. Journal of Animal Science, 89, 926-934.
  27. Machado, J. P. (2014). Evolutionary characterization of genes involved in development and adaptation in vertebrates under differential environmental conditions of selective pressure. Universidade do Porto, Rua dos Bragas, Portugal. 193pp.
  28. 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.
  29. Nielsen, R. & Yang, Z. (1998). Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 148, 929-36.
  30. Nielsen, R., Williamson, S., Kim, Y., Hubisz, M.  J., Clark, A. G. & Bustament C. (2005). Genomic scans for selective sweeps using SNP data. Genome Research, 15, 1566-1575.
  31. 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 B. Biological Sciences, 365, 185-205.
  32. Olivier, W. J., Olivier, M. A., Van Wyk, J. J. & Erasmus, G. J. (2001). Direct and correlated responses to selection for total weight of lamb weaned in Merino sheep. South African Journal of Animal Science, 31(2), 115-121.
  33. Olsen, H. G., Hayes, B. J., Kent, M. P., Nome, T., Svendsen, M. & Lien, S. (2010). A genome wide association study for QTL affecting direct and maternal effects of stillbirth and dystocia in cattle. Animal Genetics, 41, 273-280.
  34. Porto-Neto, L. R., Lee, S. H., Sonstegard, T., van Tassel, C., Lee, H. K., Gibson, J. P., et al. (2014). Genome-wide detection of signatures of selection in Korean Hanwoo cattle. Animal Genetics, 45, 180-90.
  35. 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.
  36. Qanbari, S., Pimentel, E.C.G., Tetens, J., Thaller, G., Lichtner, P., Sharifi, A. R., Simianer, H., (2010). A genome-wide scan for signatures of recent selection in Holstein cattle. Animal Genetics, 41, 377-389.
  37. Qanbari, S., Gianola, D., Hayes, B., Schenkel, F., Miller, S., Moore, S., Thaller, G., Simianer, H., (2011). Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. BMC Genomics, 12, 318.
  38. 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.
  39. Rincon, G., Farber, E. A., Farber, C. R., Nkrumah, J. D. & Medrano, J. F. (2009). Polymorphisms in theSTAT6gene and their association with carcass traits in feedlot cattle. Animal Genetics, 40, 878-882.
  40. Rubin, C.-J., Zody, M. C., Eriksson, J., Meadows, J. R. S., Sherwood, E., et al., (2010). Whole-genome resequencing reveals loci under selection during chicken domestication. Nature, 464, 587-591.
  41. Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z. P., Richter, D. J., Schaffner, S. F., et al. (2002). Detecting recent positive selection in the human genome from haplotype structure. Nature, 419, 832-837.
  42. Sabeti, P. C., Scheffner, 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, 1614-1620.
  43. 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.
  44. Suárez-Vega, A., Gutiérrez-Gil, B., Klopp, C., Tosser-Klopp, G. & José Arranz, J. (2017). Variant discovery in the sheep milk transcriptome using RNA sequencing. BMC Genomics, 18:170. DOI 10.1186/s12864-017-3581-1
  45. Sun, L., Bai, M., Xiang, L., Zhang, G., Ma, W. & Jiang, H. (2016). Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep. Scientific Reports 6:33586, DOI: 10.1038/srep33586.
  46. Sylvie, R. B. (2011). The Collagen Family. Cold Spring Harbor Perspectives in Biology, 3:a004978.
  47. Tang, K., Thornton, K.R., Stoneking, M., (2007). A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biology, 5, e171.
  48. UniProtKB Gene. http://www.uniprot.org/help/gene_name.
  49. Voight, B. F., Kudaravalli, S., Wen, X. & Pritchard, J. K. (2006). A map of recent positive selection in the human genome. PLoS Biology, 4, e72.
  50. Walter, S., Atzmon, G., Demerath, E. W., Garcia, M. E., Kaplan, R. C., Kumari, M., Lunetta, K. L., Milaneschi, Y., Tanaka, T., et al. (2011). A genome-wide association study of aging. Neurobiology of Aging. 32(11):2109.e15-28. doi: 10.1016/j.
  51. Wang, X., Liu, J., Zhou, G., Guo, J., Yan, H., Niu, Y., Li, Y., Yuan, C., Geng, R., Lan, X., An, X., Tian, X., Zhou, H., Song, J., Jiang, Y. & Chen, Y. (2016). Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits. Scientific Reports, 6:38932. DOI: 10.1038/srep38932
  52. White, S. N., Casas, E., Allan, M .F., Keele, J. W., Snelling, W. M., Wheeler, T. L., Shackelford, S. D., Koohmaraie, M. & Smith, T. P. L. (2007). Evaluation in beef cattle of six deoxyribonucleic acid markers developed for dairy traits reveals an osteopontin polymorphism associated with postweaning growth. Journal of Animal Science, 85, 1-10.
  53. Xu, L., Bickhart, D. M., Cole, J. B., Schroeder, S. G., Song, J., Van Tassell, C. P., Sonstegard, T. S. & George, E. L. (2014). Genomic Signatures Reveal New Evidences for Selection of Important Traits in Domestic Cattle. Molecular Biology and Evolution, 32(3), 711-725.
  54. Xu, H., Xu, Y., Liang, X., Wang, Y., Jin, F., Liu, D., Ma, Y., Yuan, H., Song, X. & Zeng, W. (2013). Porcine skeletal muscle differentially expressed geneATP5B: molecular characterization, expression patterns, and association analysis with meat quality traits. Mammalian Genome, 24, 142-150.
  55. Zelenchuk, L. V., Hedge, A. M. & Rowe, P. S. N. (2015). Age dependent regulation of bone‑mass and renal function by the MEPE ASARM‑motif. Bone, 79, 131-42.
  56. Zhao, F., McParland, S., Kearney, F., Du L. & Berry, D. P. (2015). Detection of selection signatures in dairy and beef cattle using high-density genomic information. Genetics Selection Evolution, 47, 49.
  57. Zhao, F. P., Wei, C. H., Zhang, L., Wang, G. K., Zeng, T. & Du, L. X. (2016). A genome scan of recent positive selection signatures in three sheep populations. Journal of Integrative Agriculture, 15(1), 162-174.
  58. 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, 20360-20374.
  59. Zhu, C., Fan, H., Yuan, Z., Hu, S., Ma, X. & et al. (2016). Genome-wide detection of CNVs in Chinese indigenous sheep with different types of tails using ovine high-density 600K SNP arrays. Scientific Reports, 6, 27822.

فایل ها

سابقه مقاله

  • تاریخ دریافت: 25 اسفند 1395
  • تاریخ بازنگری: 25 تیر 1396
  • تاریخ پذیرش: 26 تیر 1396

هم رسانی

ارجاع به این مقاله

آمار