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مطالعه پویش کل ژنوم جهت شناسایی جایگاه‌های ژنتیکی مرتبط با بیماری لکوز در گاوهای هلشتاین ایران

نوع مقاله : مقاله پژوهشی

نویسندگان

1 گروه علوم دامی، دانشکده کشاورزی، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج، ایران. رایانامه: arjmand.farnaz@ut.ac.ir

2 نویسنده مسئول، گروه علوم دامی، دانشکده کشاورزی، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج، ایران. رایانامه: hmoradis@ut.ac.ir

3 گروه علوم دامی، دانشکده کشاورزی، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج، ایران. رایانامه: moradim@ut.ac.ir

4 گروه علوم دامی، دانشکده کشاورزی و منابع طبیعی، دانشگاه اراک، اراک، ایران. رایانامه: h-mohammadi64@araku.ac.ir

5 گروه علوم دامی، دانشکده کشاورزی، پردیس بین‌المللی ارس، دانشگاه تهران، جلفا، ایران. رایانامه: javannikkhah@yahoo.com

6 گروه علوم دامی، دانشکده کشاورزی، پردیس کشاورزی و منابع طبیعی دانشگاه تهران، کرج، ایران. رایانامه: y.devisty@ut.ac.ir

چکیده

عفونت ویروس لوسمی گاوی (BLV) بیش‌تر در گله‌های شیری شیوع داشته و به‌دلیل محدودیت‌های تجاری و مرگ‌ومیر ناشی از لنفوسارکوم باعث ضررهای اقتصادی مستقیم می‌شود که هم‌چنین با کاهش تولید شیر و افزایش نرخ حذف نیز مرتبط می‌باشد.  هدف از این پژوهش، مطالعه پویش کل ژنوم (GWAS) برای شناسایی مناطق ژنومی و ژن‌های کاندیدا مرتبط با عفونت به BLV بود. این مطالعه با استفاده از گاوهای هلشتاین ایران که به‌طور طبیعی به BLV آلوده شده بودند، انجام گرفت. بدین منظور از 150 راس گاو هلشتاین در یکی از گاوداری‌های صنعتی اصفهان، نمونه‌خون جمع‌آوری و از آن‌ها استخراج DNA و سرم انجام گردید. سپس نمونه‌های DNA آماده‌شده با استفاده از تراشه‌های k30 (SNPchip30k) (توسط شرکت ایلومینا) تعیین ژنوتیپ شدند. کنترل کیفیت نشانگرهای تعیین ژنوتیپ‌شده براساس شاخص‌های فراوانی آلل نادر (05/0 PMAF <)، ژنوتیپ از دست‌رفته (05/0PMIND >)، نرخ تعیین ژنوتیپ (05/0PGENO>) و تعادل هاردی-واینبرگ (6-10×1PH-W <) توسط نرم‌افزار PLINK انجام شد. بعد از آنالیز کنترل کیفیت 145 راس گاو (77 بیمار و 68 شاهد) و 22868 نشانگر برای ادامه آنالیز باقی‌ماند. پس از انجام آنالیز پویش ژنوم در برنامه PLINK در نهایت هشت نشانگر بالاتر از حد آستانه معنی‌داری، شناخته شدند که بیش‌ترین نشانگرهای معنی‌دار در کروموزوم‌های 17 و 21 قرار داشتند. با بررسی بیوانفورماتیکی مناطق ژنومی معنی‌دار با استفاده از پایگاه‌های برخط ensemble و genecards، ژن‌های مرتبط با نشانگرهای معنی‌دار انتخاب شده، شناسایی شدند که مهم‌ترین آن‌ها GRK4، TP53BP1، ‌SCAPER، GLRB، PDGFC، TNIP2، PSTPIP1، CEP350، MR1، TOM1L2، SREBF1، COPS و TNFRS13B بود.

کلیدواژه‌ها

عنوان مقاله [English]

Genom-wide association study to identify the loci related to resistance in Leukosis disease in Iranian Holstein cattle

نویسندگان [English]

  • farnaz arjmand kermani 1
  • Hossein Moradi Shahrbabak 2
  • Mohammad Moradi Shahre Babak 3
  • hossein mohamdi 4
  • Mehdi Javan Nikkhah 5
  • younes dossti 6

1 Department of Animal Science, Faculty of Agriculture, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran. E-mail: arjmand.farnaz@ut.ac.ir, y.devisty@ut.ac.ir

2 Corresponding Author, Department of Animal Science, Faculty of Agriculture, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran. E-mail: hmoradis@ut.ac.ir

3 Department of Animal Science, Faculty of Agriculture,, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran. E-mail: moradim@ut.ac.ir

4 Assistant Professor, Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran. E-mail: h-mohammadi64@araku.ac.ir

5 Aras International Campus, University of Tehran, Jolfa, Iran. E-mail: javannikkhah@yahoo.com

6 Department of Animal Science, Faculty of Agriculture, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran. E-mail: y.devisty@ut.ac.ir

چکیده [English]

Introduction: Bovine Leukemia Virus (BLV) infection is more common in dairy cattle herds. The main cause of leukosis is the disease that leads to the creation of cancerous lymphocytes in different organisms of the body and affects different species, including cattle. This disease reduces milk production and causes reproductive diseases, and finally the removal of infected animals. Due to trade restrictions and deaths caused by lymphosarcoma, it causes direct economic losses, which is also related to the decrease in milk production and the increase in the elimination rate. No treatment or vaccine is known for this disease so far. Therfore, studying the genomic regions related to susceptibility to BLV infection can be effective in controlling and treating this disease and genetic improvement of animals. This research aimed to perform a whole genom-wide association study (GWAS) study of cattle to identify genomic regions and candidate genes associated with BLV infection.
Material and Methods This study was conducted using Holstein cows that were naturally infected with BLV. For this purpose, blood samples of 150 Holstein cows in an industrial dairy cattle farm in Isfahan were collected, and DNA and serum of them were extracted. The prepared DNA samples were genotyped using k30 microarrays (SNPchip30k) (by Illumina). Quality control of sequences for rare allele frequency components (PMAF < 0.05), missing genotype (PMIND > 0.05), genotyping rate (PGENO > 0.05), and Hardy-Weinberg equilibrium (PH-W < 1×10-6) and significance test was performed by PLINK software. Analysis of the ontology of genes was done by the online database https://www.Uniprot.org and finally, the ontology diagram of genes was drawn and analyzed by the online database PANTHER.
Results and Discussion: After control analyzing, 145 cows (77 cases and 68 controls) and 22868 markers were left for further analysis, finally 8 markers higher than the significant threshold were identified, and most significant markers were located on chromosomes 17 and 21. Using ensemble sites and genecards, genes associated with significant selected markers were identified. The most important of them were GRK4, TP53BP1, SCAPER, GLRB, PDGFC, TNIP2, PSTPIP1, CEP350, MR1, TOM1L2, SREBF1, COPS and TNFRS13B. Gene Ontology (GO) analysis showed that these genes are more involved in protein-coding and play a role in regulating enzyme activities, intercellular exchanges, DNA stability, calcium activity, nervous system, and lipid activity. Also, according to other research, these genes played a role in cases such as infectious poison lesions, subclinical ketosis disease, BCS of cattle, fatty acid metabolism and fat deposition, various infections such as mastitis, and in meat traits and muscle stiffness in beef cattle. It should be noted that some of these genes were related to the pathways of innate immunity, humoral immunity, and cancer tumors.
Conclusion: Therefore, it can be concluded that whole genome wide association study analysis as well as gene ontology analysis to identify genomic regions related to viral infections such as leukemia can be effective in designing treatment methods and prevention methods and in choosing Genomics and breeding programs in Iranian dairy cows.

کلیدواژه‌ها [English]

  • Bovine Leukemia
  • Genotype
  • GWAS
  • Lymphocyte
  • SNP
مراجع
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تولیدات دامی
دوره 26، شماره 3
مهر 1403
صفحه 219-232
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هم رسانی
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