بازسازی شبکه‌های ژنی و برهم کنش پروتئینی دخیل در پاسخ به تنش خشکی در برنج

نوع مقاله: علمی پژوهشی

نویسندگان

1 کارشناسی‌ارشد، گروه زیست‌شناسی سیستم‌ها، پژوهشگاه بیوتکنولوژی کشاورزی ایران، سازمان تحقیقات، آموزش و ترویج کشاورزی، کرج، ایران

2 2. استادیار گروه زیست‌شناسی سیستم‌ها، پژوهشگاه بیوتکنولوژی کشاورزی ایران، سازمان تحقیقات، آموزش و ترویج کشاورزی، کرج، ایران

چکیده

برنج یکی از ارزشمندترین محصولات کشاورزی است. یکی از تأثیرگذارترین عوامل محدود کننده این محصول استراتژیک تنش خشکی می‌باشد. نظر به چند ژنی بودن تحمل به خشکی، هدف پژوهش حاضر بازسازی شبکه ژنی درگیر و شناسایی ژن‌های کلیدی مربوطه در برنج با استفاده از تجزیه و تحلیل داده‌های ریزآرایه بوده است. به همین منظور با استفاده از نرم‌افزار تحت وب Genevestigator تمامی ژن‌های دارای تغییر بیان بالاتر و مساوی 5/2 و پایین‌تر و مساوی 5/2- در حالت تنش خشکی نسبت به شرایط نرمال در بین تمامی آزمایشات ریزآرایه انجام شده در برنج شناسایی شدند. در مجموع 101 ژن با تغییر بیان ≥5/2 و ≤5/2- شناسایی شد و شبکه تنظیم ژنی و برهم‌کنش پروتئینی برای آن‌ها رسم گردید. ژن‌های قطب (ژن‌های دارای بیشترین برهم‌کنش) با استفاده از 9 الگوریتم محاسباتی Cyto-Hubba در نرم‌افزار Cytoscape شناسایی شدند. این امر منجر به شناسایی 14 ژن غیر تکراری شد که به عنوان مؤثرترین ژن‌ها در پاسخ به تنش خشکی در نظر گرفته شدند و شبکه هم‌بیانی آن‌ها رسم گردید. بر اساس بررسی هستی‌شناسی ژن‌های دارای بیان افتراقی، ژن‌های هم بیان با آنها و ژن‌های قطب، تنظیم رونویسی از گروه‌های اصلی بود که نشان دهنده اهمیت عوامل رونویسی در مکانیسم تحمل به خشکی می‌باشد. در میان عوامل رونویسی می‌توان به عوامل پاسخ دهنده به تنش خشکی همچون خانواده‌های ژنی AP2، bZIP، WRKY، MYB و عوامل متصل شونده به عناصر پاسخ دهنده به ABA، اشاره نمود. امید است نتایج به‌دست آمده در راستای یافتن راهکارهایی هدفمند جهت افزایش تحمل به خشکی مفید واقع گردد.

کلیدواژه‌ها

موضوعات


عنوان مقاله [English]

Reconstruction of drought responsive gene and protein interaction networks in rice

نویسندگان [English]

  • Ehsan Pourabed 1
  • Zahra-Sadat Shobbar 2
1 M.Sc., Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
2 Assistant Professor, Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Education and Extension Organization (AREEO), Karaj, Iran.
چکیده [English]

Rice is one of the most valuable crops, and water deficiency is the most important constraint to rice production. Due to the complexity and multigenic characteristics of the drought tolerance trait, the objective of the current research were reconstruction of the involved gene networks and identification of the key genes in rice plants using microarray data analysis. To achieve the goal, all the differentially expressed genes (DEGs) with fold changes ≥+2.5 and ≤-2.5 at drought stress compared to normal conditions were identified among all the microarray data-series in rice using Genevestigator online tools. Totally, 101 DEGs were identified and their gene regulatory as well as protein-protein interactions (PPIs) networks was reconstructed. The hub genes (genes with the most interactions) were distinguished using nine Cyto-hubba computational algorithms on Cytoscape software. Based on the hub analysis results, 14 unique (non-redundant) genes were identified as the most effective genes in response to drought stress and their co-expression networks were constructed. According to the gene ontology analysis of the DEGs, their co-expressed genes and the hub genes, regulation of transcription were among the major groups indicating the importance of transcription factors (TFs) roles in drought tolerance mechanism. Amongst the TFs, ABA-responsive binding factors (AREBs), AP2, bZIP, WRKY and MYB gene families were observed. We hope that the obtained results would be beneficial toward finding the smart strategies for drought tolerance improvement.

کلیدواژه‌ها [English]

  • Biological network
  • drought responsive genes
  • Hub gene
  • Microarray
  • Oryza sativa

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