آنالیز بیوانفورماتیکی ژن‌های کاندید موثر بر چند قلوزایی و تولید شیر در بز

نوع مقاله : مقاله پژوهشی

نویسندگان

1 دانش‌آموخته کارشناسی‌ارشد، گروه علوم دامی، دانشکده علوم دامی و شیلات، دانشگاه علوم کشاورزی و منابع طبیعی ساری،

2 دانشیار ، گروه علوم دامی، دانشکده علوم دامی و شیلات، دانشگاه علوم کشاورزی و منابع طبیعی ساری،

3 استاد، گروه علوم دامی، دانشکده علوم دامی و شیلات، دانشگاه علوم کشاورزی و منابع طبیعی ساری، ساری، ایران

4 پژوهشگر، مرکز ایمنی و ایمونوتراپی، موسسه تحقیقات کودکان سیاتل، سیاتل، ایالات متحده آمریکا

چکیده

سابقه و هدف: تولید شیر و صفات تولیدمثلی از صفات اقتصادی مهم در بز می باشند. در حال حاضر رویکردهای مختلف از جمله نقشه‌یابی ژن کاندید و مطالعات ژنومی برای شناسایی مکانیسم‌های مولکولی مؤثر بر این صفات مهم اقتصادی در بز انجام می‌شود. تجزیه‌و‌تحلیل هستی‌شناسی ژن، امکان توصیف ویژگی‌های ژن‌ها و محصولات ژنی را به شکل طبقه‌بندی شده و قابل‌فهم‌تر ارائه می دهد. آنالیز KEGG، رویکردی را برای بررسی دقیق عملکردهای ژن در رابطه با شبکه‌های ژنی با استفاده از داده‌های مولکولی ارائه می‌دهد. تجزیه‌و‌تحلیل شبکه ژنی، هم‌چنین می‌تواند مسیرها و فرآیندهای مولکولی مشترک ژن‌های کاندید را شناسایی کند. هدف از پژوهش حاضر آنالیز بیوانفورماتیکی (هستی‌شناسی ژن، مسیرهای بیولوژیکی، و تجزیه و تحلیل شبکه برهم‌کنش پروتئین-پروتئین) ژن‌های مؤثر بر چندقلوزایی و تولید شیر در بز بود.
مواد و روش‌ها: ابتدا با بررسی منابع، شامل مطالعات انجام شده روی ژن‌های کاندیدا، مطالعات پویش کامل ژنومی و پایگاه‌ داده NCBI، ژن‌های موثر بر چندقلوزایی و تولید شیر در بز جمع‌آوری شدند. آنالیز هستی‌شناسی ژن و آنالیز غنی‌سازی مسیر KEGG، ژن‌های کاندید با استفاده از پایگاه داده g: Profiler انجام شد. پایگاه داده STRING، برای تشکیل شبکه برهم‌کنش پروتئین-پروتئین و انتخاب ماژول عملکرد مورد استفاده قرار گرفت. از نرم‌افزار Cytoscape، برای ترسیم شبکه اثرات متقابل پروتئین-پروتئین استفاده شد. در نهایت از افزونه cytoHubba جهت شناسایی ژن‌های کلیدی استفاده شد.
یافته‌ها: آنالیز هستی‌شناسی ژن نشان داد که برای صفت چندقلوزایی، ژن‌های کاندید مورد مطالعه برای عملکردهای مولکولی در مسیرهای اتصال گیرنده سیگنالی، فعالیت گیرنده سیگنالی، فعالیت هورمونی، اتصال پروتئین و فعالیت گیرنده فاکتور رشد تغییردهنده بتا غنی شدند. همچنین آنالیز KEGG، مسیرهای سیگنالی متعددی از جمله برهم‌کنش گیرنده سیتوکین-سیتوکین، PI3K-Akt، TGF-بتا و استروئیدوژنز تخمدان را شناسایی نمود که با چندقلوزایی در گونه‌های مختلف پستانداران در ارتباط هستند. تأثیر خانواده تبدیل‌کننده فاکتور رشدβ ، بر باروری و تولید‌مثل، رشد جنینی، اندام‌زایی، و رشد و عملکرد رحم در طیف وسیعی از موجودات چشمگیر است. در پستانداران، حتی مراحل اولیه رشد تولیدمثلی، از جمله تمایز ژرم لاین نر و ماده، توسط پروتئین‌های مربوط به TGF-β کنترل می‌شو‌ند. باندشونده‎های هورمون نقش مهمی در بر باروری و تولید مثل ایفا می‌کنند. گلوبولین باندشونده به هورمون جنسی، به طور خاص به آندروژن‌ها و استروژن‌های فعال بیولوژیکی متصل می‌شوند که تنظیم‌کننده‌های کلیدی اندام‌های تناسلی و سایر بافت‌های دارای تفاوت جنسی مانند ماهیچه، بافت چربی و استخوان هستند. آنالیز غنی‌سازی مجموعه‌های ژنی برای تعداد 33 ژن کاندید مرتبط با صفت تولید شیر، تنها یک طبقه هستی‌شناسی ژن برای مسیر زیستیِ فرآیند متابولیک اسید لینولئیک را شناسایی نمود.
نتیجه‌گیری: در این مطالعه، چندین مسیر زیستی معنی‌دار و مسیرهای سیگنالی را شناسایی شد که می توانند برای درک بهتر فرآیندهای زیستی مرتبط با صفات چندقلوزایی و تولید شیر در بز مورد استفاده قرار گیرند.

کلیدواژه‌ها

موضوعات


عنوان مقاله [English]

Bioinformatics analysis of candidate genes for milk production and littersize in goat

نویسندگان [English]

  • Bahram Afzali-talkhak 1
  • Mohsen Gholizadeh 2
  • Hassan, Hafezian 3
  • Mehdi Esmaeili-fard 4
1 Master student, Department of Animal Science, Faculty of Animal Science and Fisheries, Sari University of Agricultural Sciences and Natural Resources.
2 Associate Professor, Department of Animal Science, Faculty of Animal Science and Fisheries, Sari University of Agricultural Sciences and Natural Resources,
3 Professor, Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
4 Researcher, Center for Immunity and Immunotherapy, Seattle Children's Research Institute, Seattle, USA
چکیده [English]

Background and Objectives: Milk production and reproductive traits are important economic traits in goat. The different approaches including candidate gene mapping and genome-wide association studies (GWAS) are now implemented in goats in an attempt to identify the molecular mechanisms affecting these economically important traits. The gene ontology (GO) analysis gives a controlled vocabulary for describing attributes of genes and gene products. Kyoto Encyclopedia of Genes and Genomes (KEGG) provides the mythology for the careful examination of gene functions in respect of networks of genes and molecules. Gene network analysis can also identify paths and processes shared by candidate genes. The purpose of the present study was to bioinformatics analysis (GO, path enrichment, and network analysis of the effects of protein-protein interaction) of genes effective in litter size and milk production in goat.
Materials and Methods: Candidate genes associated with studied traits were retrieved from literature review, review of candidate gene studies, GWAS and NCBI database. GO analysis and enrichment analysis of the signaling pathways of KEGG were performed using online database of G: Profiler. The String database was used to infer the network of protein-protein interactions (PPI) and the selection of performance module. Cytoscape software was used to draw the resultant networks of protein-protein interactions. Finally, cytoHubba was used to identify Hub genes.
Results: GO analysis for litter size showed that, for molecular function the candidates genes enriched in signaling receptor binding, signaling receptor active activity, hormone activity, protein binding and transforming growth factor beta receptor activity. The effect of the transforming growth factor β (TGF-β) family on fertility and reproduction, embryonic development, organogenesis, and uterine growth and function is remarkable in a wide range of organisms. In mammals, even early stages of reproductive development, including male and female germline specification, are controlled by TGF-β-related proteins. Hormone binding play an important role in fertility and reproduction. Sex hormone-binding globulin (SHBG), specifically bound to the biologically active androgens and estrogens that are key regulators of the reproductive organs as well as other sex-differentiated tissues such as muscle, adipose tissue, and bone. KEGG analysis also identified some signaling pathways including ، PI3K-Akt signaling pathway، TGF-beta signaling pathway and ovarian steroidogenesis which are significantly associated with litter size. GO analysis for 33 candidate genes related to milk production traits identified only one GO category for biological process namely linoleic acid metabolic process.
Conclusion: In this study, we identified several significant biological and signaling pathways that can be used to better understand the biological processes associated with litter size and milk production in goats.

کلیدواژه‌ها [English]

  • Goat
  • litter size
  • Gene network analysis
  • Candidate gene
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