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شناسایی نواحی ژنومی تحت انتخاب مثبت برای سازگاری با ارتفاع بالا در گوسفندان ایرانی | ||
علوم دامی ایران | ||
دوره 55، شماره 1، فروردین 1403، صفحه 143-162 اصل مقاله (1.86 M) | ||
نوع مقاله: مقاله پژوهشی | ||
شناسه دیجیتال (DOI): 10.22059/ijas.2023.353223.653925 | ||
نویسندگان | ||
زهرا پتی آبادی1؛ محمد رزم کبیر* 1؛ علی اسمعیلی زاده کشکوئیه2؛ محمدحسین مرادی3؛ امیر رشیدی4 | ||
1گروه علوم دامی، دانشکده کشاورزی، دانشگاه کردستان، سنندج، ایران | ||
2گروه علوم دامی، دانشکده کشاورزی، دانشگاه شهید باهنر کرمان، کرمان، ایران | ||
3گروه علوم دامی، دانشکده کشاورزی، دانشگاه اراک، اراک، ایران | ||
4گروه علوم دامی، دانشکده کشاورزی، دانشگاه کردستان، سنندج، ایران. | ||
چکیده | ||
شناسایی نشانههای انتخاب، اطلاعاتی در مورد مراحل تکامل گونههای مختلف از جمله گوسفند، که منجر به تغییراتی در سطح ژنوم آنها در طی سالیان متمادی میشود، را فراهم میکند. هدف از این پژوهش شناسایی نشانههای ژنومی انتخاب در گوسفندان مناطق مرتفع کشور ایران بود. بدین منظور 58 رأس گوسفند از 4 نژاد که دو نژاد در مناطق مرتفع و دو نژاد در مناطق پست پراکندهاند، با استفاده از آرایههای گوسفندk 600 تعیین ژنوتیپ شدند. جهت شناسایی نواحی ژنومی تحت انتخاب از دو آزمون آماری برآوردگر نااریب FST (تتا) و hapFLK استفاده شد. با استفاده از آزمون تتا، 22 منطقه ژنومی به عنوان مناطق تحت انتخاب شناسایی شدند. در آزمون hapFLK نیز 15 منطقه ژنومی شناسایی شد. تجزیه و تحلیل اطلاعات زیستی (بیوانفورماتیکی) نشان داد که برخی از این مناطق ژنومی با ژنهای موثر بر سازگاری با شرایط کم اکسیژنی (TXNDC5)، خونسازی (FANCA)، ایمنیزایی و مقابله با عفونت (LEF1، NMUR1، PTMA و COPS7B)، تنظیم فشار خون و پاسخ به درد و التهاب (NMUR1) و سرکوب سرطان (CD82، GAS8، PRMT1، B3GNT7 و ...) همپوشانی دارند. بررسی QTLهای گزارش شده نیز نشان داد که این مناطق با QTLهای صفات مهم اقتصادی از جمله صفات مرتبط با میانگین غلظت هموگلوبین گلبولهای قرمز، هماتوکریت، مشخصات گوشت، لاشه، شیر، وزن بدن، تراکم استخوان و تعداد کل برههای متولد شده در ارتباط میباشند. با توجه به اینکه تحقیقات کمی در رابطه با سازگاری با ارتفاع در گوسفندان انجام شده است، لذا نتایج این تحقیق میتواند اطلاعات سودمندی در رابطه با ژنهایی که به سازگاری با ارتفاع پاسخ میدهند، ارایه دهد. به هر حال، به منظور شناسایی و بررسی دقیقتر جهشهای عامل در ژنها و QTLهای شناسایی شده ضروری است که پژوهشهای تکمیلی بیشتری صورت گیرد. | ||
کلیدواژهها | ||
آزمون FST؛ آزمون hapFLK؛ ارتفاع از سطح دریا؛ پویش ژنومی؛ نشانههای انتخاب | ||
مراجع | ||
Adachi, M., Taki, T., leki, Y., Huang, C., HigasMyama, M. & Miyake, M. (1996). Correlation of KAI1/CD82 Gene Expression with Good Prognosis in Patients with Non-Small Cell Lung Cancer. Cancer Research, 56(8), 1751-1755. Akey, J.M. (2009). Constructing genomic maps of positive selection in humans. Where do we go from here? Genome Research, 19, 711-722. Akey, J. M., Zhang, G., Zhang, K., Jin, L., & Shriver, M. D. (2002). Interrogating a high-density SNP map for signatures of natural selection. Genome Research, 12(12), 1805-1814. Alberts, B. (2008). Molecular Biology of the Cell (5th ed.). New York: Garland Science. 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. Bidhendi, A. J., Altartouri, B., Gosselin, F. P., & Geitmann, A. (2019). Mechanical stress initiates and sustains the morphogenesis of wavy leaf epidermal cells. Cell Reports, 28(5), 1237-1250. Biswas, S. & Akey, J. M. (2006). Genomic insights into positive selection. Trends in Genetics, 22, 437-436. 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(1), 241-262. Brighton, P. J., Szekeres, P. G. & Willars, G. B. (2004). Neuromedin U and its receptors: structure, function, and physiological roles. Pharmacol, 56 (2), 231–48. Büdinger, L., Hertl, M., & Büdinger, L. (2000). Immunologic mechanisms in hypersensitivity reactions to metal ions: an overview. Allergy, 55(2), 108-115. Carroll, D. J., Burns, M. W., Mottram, L., Propheter, D. C., Boucher, A., Lessen, G. M., ... & Kohler, J. J. (2022). Interleukin-22 regulates B3GNT7 expression to induce fucosylation of glycoproteins in intestinal epithelial cells. Journal of Biological Chemistry, 298(2). Crow, T. J., & Kelman, G. R. (1973). Psychological effects of mild acute hypoxia. British Journal of Anaesthesia, 45(4), 335-337. Dennis, J. W., Granovsky, M., & Warren, C. E. (1999). Protein glycosylation in development and disease. Bioessays, 21(5), 412-421. Duran-Nebreda, S., Pla, J., Vidiella, B., Piñero, J., Conde-Pueyo, N., & Solé, R. (2021). Synthetic lateral inhibition in periodic pattern forming microbial colonies. ACS Synthetic Biology, 10(2), 277-285. Edea, Z., Dessie, T., Dadi, H., Do, K. T., & Kim, K. S. (2017). Genetic diversity and population structure of Ethiopian sheep populations revealed by high-density SNP markers. Frontiers in Genetics, 8, 218. Endo, M. (2006). Calcium ion as a second messenger with special reference to excitation-contraction coupling. Journal of Pharmacological Sciences, 100(5), 519-524. Faramoushi, M., Amir Sasan, R., Sari Sarraf, V., & Karimi, P. (2016). Effect of simulated intermittent altitude on the metabolic and hematologic parameters in streptozotocin induced diabetic rats. Journal of Ardabil University of Medical Sciences, 16(1), 53-64. Fariello, M. I., Boitard, S., Naya, H., SanCristobal, M., & Servin, B. (2013). Detecting signatures of selection through haplotype differentiation among hierarchically structured populations. Genetics, 193(3), 929-941. Fededa, J. P., & Gerlich, D. W. (2012). Molecular control of animal cell cytokinesis. Nature Cell Biology, 14(5), 440-447. Galardi, S., Fatica, A., Bachi, A., Scaloni, A., Presutti, C., & Bozzoni, I. (2002). Purified box C/D snoRNPs are able to reproduce site-specific 2′-O-methylation of target RNA in vitro. Molecular and Cellular Biology, 22(19), 6663-6668. Gale, G. E., Torre-Bueno, J. R., Moon, R. E., Saltzman, H. A., & Wagner, P. D. (1985). Ventilation-perfusion inequality in normal humans during exercise at sea level and simulated altitude. Journal of Applied Physiology, 58(3), 978-988. Gardner, J. L., Peters, A., Kearney, M., Joseph, L., & Heinsohn, R. (2011). Declining body size: a third universal response to warming? Trends in Ecology & Evolution, 26(6), 285-291. Gebreselassie, G., Liang, B., Berihulay, H., Islam, R., Abied, A., Jiang, L., ... & Ma, Y. (2020). Genomic mapping identifies two genetic variants in the MC1R gene for coat colour variation in Chinese Tan sheep. PloS One, 15(8), e0235426. Gene Cards. http://www.genecards.org/cgi-bin/carddisp.pl?gene=STAT. Goldstein, A. L., & Goldstein, A. L. (2009). From lab to bedside: emerging clinical applications of thymosin α1. Expert Opinion on Biological Therapy, 9(5), 593-608. Gorkhali, N. A., Dong, K., Yang, M., Song, S., Kader, A., Shrestha, B. S., ... & Ma, Y. (2016). Genomic analysis identified a potential novel molecular mechanism for high-altitude adaptation in sheep at the Himalayas. Scientific Reports, 6(1), 1-10. Grossman, S. R., Shylakhter, I., Karlsson, E. K., Byrne, E. H., Morales, S., Frieden, G., ... & Sabeti, P. C. (2010). A composite of multiple signals distinguishes causal variants in regions of positive selection. Science, 327(5967), 883-886. Guen, V. J., Gamble, C., Flajolet, M., Unger, S., Thollet, A., Ferandin, Y., ... & Colas, P. (2013). CDK10/cyclin M is a protein kinase that controls ETS2 degradation and is deficient in STAR syndrome. Proceedings of the National Academy of Sciences, 110(48), 19525-19530. Hancock, A. M., Witonsky, D. B., Alkorta-Aranburu, G., Beall, C. M., Gebremedhin, A., Sukernik, R., ... & Di Rienzo, A. (2011). Adaptations to climate-mediated selective pressures in humans. PLoS Genetics, 7(4), e1001375. Hoffmann, I. (2010). Climate change in context: implications for livestock production and diversity. Edited by NE Odongo, M. Garcia & GJ Viljoen, 33. Horna-Terrón, E., Pradilla-Dieste, A., Sánchez-de-Diego, C., & Osada, J. (2014). TXNDC5, a newly discovered disulfide isomerase with a key role in cell physiology and pathology. International Journal of Molecular Sciences, 15(12), 23501-23518. Joost, S., Bonin, A., Bruford, M. W., Després, L., Conord, C., Erhardt, G., & Taberlet, P. (2007). A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Molecular Ecology, 16(18), 3955-3969. Kageyama, T., Nagashio, R., Ryuge, S., Matsumoto, T., Iyoda, A., Satoh, Y., ... & Sato, Y. (2011). HADHA is a potential predictor of response to platinum-based chemotherapy for lung cancer. Asian Pacific Journal of Cancer Prevention, 12(12), 3457-63. Karell, P., Ahola, K., Karstinen, T., Valkama, J., & Brommer, J. E. (2011). Climate change drives microevolution in a wild bird. Nature Communications, 2(1), 1-7. Kayserili, H., Uz, E., Niessen, C., Vargel, I., Alanay, Y., Tuncbilek, G., ... & Akarsu, N. A. (2009). ALX4 dysfunction disrupts craniofacial and epidermal development. Human Molecular Genetics, 18(22), 4357-4366. Klose, C, S., Mahlakõiv, T., Moeller, J. B., Rankin, L. C., Flamar, A. L., Kabata, H., ... & Artis, D. (2017). The neuropeptide neuromedin U stimulates innate lymphoid cells and type 2 inflammation. Nature, 549(7671), 282-286. Kreitman, M. (2000). Methods to detect selection in populations with applications. The Annual Review of Genomics and Human Genetics, 1, 539-59. Latour, B. L., Van, De., Weghe, J. C., Rusterholz, T. D., Letteboer, S. J., Gomez, A., Shaheen, R., Gesemann, M., Grout, M. E., van Reeuwijk, J., Van Beersum, S. E. & Miller, C. V. (2019). ARMC9 and TOGARAM1 define a Joubert syndrome-associated protein module that regulates axonemal post-translational modifications and cilium stability. BioRxiv, 1, 817213. Li, J., Belogortseva, N., Porter, D., & Park, M. (2008). Chmp1A functions as a novel tumor suppressor gene in human embryonic kidney and ductal pancreatic tumor cells. Cell Cycle, 7(18), 2886-2893. Lobell, D. B., Burke, M. B., Tebaldi, C., Mastrandrea, M. D., Falcon, W. P., & Naylor, R. L. (2008). Prioritizing climate change adaptation needs for food security in 2030. Science, 319(5863), 607-610. 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(1), 1-19. Mastrangelo, S., Bahbahani, H., Moioli, B., Ahbara, A., Al Abri, M., Almathen, F., ... & Ciani, E. (2019). Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia. PLoS One, 14(6), e0209632. Mathioudaki, K., Papadokostopoulou, A., Scorilas, A., Xynopoulos, D., Agnanti, N., & Talieri, M. (2008). The PRMT1 gene expression pattern in colon cancer. British Journal of Cancer, 99(12), 2094-2099. McCormick, C., Duncan, G., Goutsos, K. T., & Tufaro, F. (2000). The putative tumor suppressors EXT1 and EXT2 form a stable complex that accumulates in the Golgi apparatus and catalyzes the synthesis of heparan sulfate. Proceedings of the National Academy of Sciences, 97(2), 668-673. McDownald, P. R., Edwards, J. F., Greenhalgh, D. & Morgan, C. A. (2006). Animal Nutrition.1st Ed. minerals. 760 p. Mochida, G. H., Ganesh, V. S., De Michelena, M. I., Dias, H., Atabay, K. D., Kathrein, K. L., ... & Walsh, C. A. (2012). CHMP1A encodes an essential regulator of BMI1-INK4A in cerebellar development. Nature Genetics, 44(11), 1260-1264. Mohammadi, H., Rafat, A., Moradi Shahre Babak, M. Shoja, J. & Moradi, M. H. (2018). Scanning the whole genus to determine positively selected sites in Zandi sheep. Iranian Journal of Animal Science, 48(4), 533-548. Mohammapdour R, Ghandehari H. (2022). Mechanisms of immune response to inorganic nanoparticles and their degradation products. Advanced Drug Delivery Reviews, 1(180): 114022. Moon, R. E. (2005). Clinical care in altered environments: at high and low pressure and in space. Miller's Anesthesia, 2665-2701. Moradi, M. H., Khaltabadi-Farahani, A. H., Khodaei-Motlagh, M., Kazemi-Bonchenari, M., & McEwan, J. (2022). Genome-wide selection of discriminant SNP markers for breed assignment in indigenous sheep breeds. Annals of Animal Science, 21(3), 807-831. 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(1), 1-15. Naggert, J. K., Fricker, L. D., Varlamov, O., Nishina, P. M., Rouille, Y., Steiner, D. F., ... & Leiter, E. H. (1995). Hyperproinsulinaemia in obese fat/fat mice associated with a carboxypeptidase E mutation which reduces enzyme activity. Nature Genetics, 10(2), 135-142. Nasoori, A. (2020). Formation, structure, and function of extra‐skeletal bones in mammals. Biological Reviews, 95(4), 986-1019. Nielsen, R. (2005). Molecular signature of natural selection. Annual Review of Genetics, 39, 197-218. 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(1537), 185-205. Pan, W., Zhang, N., Liu, W., Liu, J., Zhou, L., Liu, Y., & Yang, M. (2018). The long noncoding RNA GAS8-AS1 suppresses hepatocarcinogenesis by epigenetically activating the tumor suppressor GAS8. Journal of Biological Chemistry, 293(44), 17154-17165. Panman, L., Drenth, T., Tewelscher, P., Zuniga, A., & Zeller, R. (2004). Genetic interaction of Gli3 and Alx4 during limb development. International Journal of Developmental Biology, 49(4), 443-448. Pavlidis, P., & Alachiotis, N. (2017). A survey of methods and tools to detect recent and strong positive selection. Journal of Biological Research-Thessaloniki, 24(1), 1-17. Pfeffer, G., Gorman, G. S., Griffin, H., Kurzawa-Akanbi, M., Blakely, E. L., Wilson, I., ... & Chinnery, P. F. (2014). Mutations in the SPG7 gene cause chronic progressive external ophthalmoplegia through disordered mitochondrial DNA maintenance. Brain, 137(5), 1323-1336. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., 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. Qanbari, S., Pausch, H., Janse, S., Somel, M., Strom, T.M., Fries, R., Nielsen, R. & Simianer, H. (2014). Classic Selective Sweeps Revealed by Massive Sequencing in Cattle. PLoS Genetics,10, 41-48. Rasmussen, H. (1985). Calcium Ion. InCalcium in biological systems, pp. 13-22. Ready, S. (2013). Abnormal Growth of the Parasite Toxoplasma Gondii in Human Cells. Ridder, K., Keller, S., Dams, M., Rupp, A. K., Schlaudraff, J., Del Turco, D., ... & Momma, S. (2014). Extracellular vesicle-mediated transfer of genetic information between the hematopoietic system and the brain in response to inflammation. PLoS Biology, 12(6), e1001874. Rossberg, W., Saternus, R., Wagenpfeil, S., Kleber, M., März, W., Reichrath, S., ... & Reichrath, J. (2016). Human pigmentation, cutaneous vitamin D synthesis and evolution: variants of genes (SNPs) involved in skin pigmentation are associated with 25 (OH) D serum concentration. Anticancer Research, 36(3), 1429-1437. Samuel, S., & Gary, W. (2011). Polar bodies—more a lack of understanding than a lack of respect. Molecular Reproduction and Development, 78(1), 3-8. Senniappan, S., Shanti, B., James, C., & Hussain, K. (2012). Hyperinsulinaemic hypoglycaemia: genetic mechanisms, diagnosis and management. Journal of Inherited Metabolic Disease, 35(4), 589-601. Shi, H., Hudson, L. G., & Liu, K. J. (2004). Oxidative stress and apoptosis in metal ion-induced carcinogenesis. Free Radical Biology and Medicine, 37(5), 582-593. Sinha, N., Puri, P., Nairn, A. C., & Vijayaraghavan, S. (2013). Selective ablation of Ppp1cc gene in testicular germ cells causes oligo-teratozoospermia and infertility in mice. Biology of Reproduction, 89(5), 128-1. Steinke, F. C., & Xue, H. H. (2014). From inception to output, Tcf1 and Lef1 safeguard development of T cells and innate immune cells. Immunologic Research, 59(1), 45-55. Stowell, S. R., Ju, T., & Cummings, R. D. (2015). Protein glycosylation in cancer. Annual Review of Pathology, 10, 473. Tan, J., & Yang, L. (2018). Long noncoding RNA VPS9D1-AS1 overexpression predicts a poor prognosis in non-small cell lung cancer. Biomedicine & Pharmacotherapy, 106, 1600-1606. Tischfield, M. A., Baris, H. N., Wu, C., Rudolph, G., Van Maldergem, L., He, W., ... & Engle, E. C. (2010). Human TUBB3 mutations perturb microtubule dynamics, kinesin interactions, and axon guidance. Cell, 140(1), 74-87. Tischkowitz, M. D., and Hodgson, S. V. (2003). Fanconi anaemia. Journal of Medical Genetics, 40, 1-10. Torres, R., Croll, S. D., Vercollone, J., Reinhardt, J., Griffiths, J., Zabski, S., ... & Murphy, A. J. (2007). Mice genetically deficient in neuromedin U receptor 2, but not neuromedin U receptor 1, have impaired nociceptive responses. Pain, 130(3), 267-278. Wara, D. W., Goldstein, A. L., Doyle, N. E., & Ammann, A. J. (1975). Thymosin activity in patients with cellular immunodeficiency. New England Journal of Medicine, 292(2), 70-74. Wei, P., Wang, H., Li, Y., & Guo, R. (2021). Nucleolar small molecule RNA SNORA75 promotes endometrial receptivity by regulating the function of miR-146a-3p and ZNF23. Aging (Albany NY), 13(11), 14924. Weir, B. S., & Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. evolution, 1358-1370. Wong, C. H. (2005). Protein glycosylation: new challenges and opportunities. The Journal of Organic Chemistry, 70(11), 4219-4225. Wu, X., Jia, J., & You, H. (2015). Thymosin alpha-1 treatment in chronic hepatitis B. Expert Opinion on Biological Therapy, 15(sup1), 129-132. Xiaowei, W. A., & Qing, M. A. (2020). Genome-wide association studies for coat color in Tan sheep. Acta Agriculturae Zhejiangensis, 32(1), 28. Yang, Y. (2009). Skeletal morphogenesis during embryonic development. Critical Reviews™ in Eukaryotic Gene Expression, 19(3). Yang, Y. (2013). Skeletal morphogenesis and embryonic development. Primer on the metabolic bone diseases and disorders of mineral metabolism, 1-14. Zhang, H., Li, S., Doan, T., Rieke, F., Detwiler, P. B., Frederick, J. M., & Baehr, W. (2007). Deletion of PrBP/δ impedes transport of GRK1 and PDE6 catalytic subunits to photoreceptor outer segments. Proceedings of the National Academy of Sciences, 104(21), 8857-8862. Zhang, L., Hou, Y., Li, N., Wu, K., & Zhai, J. (2010). The influence of TXNDC5 gene on gastric cancer cell. Journal of Cancer Research and Clinical Oncology, 136(10), 1497-1505. | ||
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