پیش‌بینی محاسباتی ژن های پاسخ دهنده به سرما در کلزا از طریق مقایسه ژنومی با گیاه مدل Arabidopsis thaliana

نوع مقاله : علمی پژوهشی

نویسندگان

1 دانشجوی دکتری بیوتکنولوژی گیاهی، دانشکده کشاورزی، دانشگاه گیلان، ایران

2 استاد گروه بیوتکنولوژی، دانشکده کشاورزی، دانشگاه گیلان، ایران

3 استادیار، دانشکده کشاورزی، دانشگاه گیلان، ایران

4 استادیار، گروه زیست شناسی سلولی و مولکولی، دانشکده علوم و فناوری زیستی، دانشگاه شهید بهشتی، ایران

چکیده

سرما تنش مهمی است که تولید و پراکندگی جغرافیایی بسیاری از گیاهان زراعی از جمله کلزا به عنوان یک گیاه روغنی مهم را محدود می‌کند. در این مقاله عناصر سیس شناخته شده که تنظیم‌کننده پاسخ مولکولی گیاه به تنش سرما هستند، برای شناسایی ژن‌های دخیل در تحمل سرما استفاده شدند. از تعداد 62384 یونیژن از پایگاه داده Brassica Genome Gateway، تعداد 56 عدد ژن مسئول سرما شناسایی شدند. برای اعتبارسنجی ژن‌های شناسایی شده آنالیز پروموتر، هستی‌شناسی، هم‌بیانی، برهمکنش پروتئین-پروتئین و آنالیز بیان ژن به صورت پیش‌بینی محاسباتی انجام شد. نتایج حاکی از حضور عناصر سیس معمول پاسخ به سرما در ناحیه پروموتر تمامی ژن‌های شناسایی شده بود که در مسیرهای مختلف زیستی مانند چرخه کالوین، تنفس سلولی و مسیرهای انتقال پیام در بخش‌های مختلف سلول قرار داشتند. بررسی هم‌بیانی ژن‌های شناسایی‌شده، اثر متقابل ژن‌ها را با همبستگی بالای 64/0 نشان داد. بررسی پروموتر، شبکه برهمکنش پروتئین-پروتئین و بررسی فاکتورهای رونویسی دخیل در تنظیم رونویسی56 عدد ژن‌ شناسایی شده و 98 عدد ژن‌ هم‌بیان آن‌ها حاکی از سازوکار مولکولی و مسیرهای مشابه و مشترک پاسخ به تنش سرما در گیاه است و ژن‌های کاندید جهت بهره‌برداری در برنامه‌های اصلاحی و مهندسی ژنتیک کلزا را معرفی می‌کند.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

In silico prediction of cold responsive genes in canola by comparative genomics using Arabidopsis thaliana

نویسندگان [English]

  • Khazar Edrisi Maryan 1
  • Habibollah Samizadeh Lahiji 2
  • Hassan Hasani Komeleh 3
  • Naser Farrokhi 4
1 Ph.D. Candidate of Plant Biotechnology, Faculty of Agriculture, University of Guilan, Rasht, Iran.
2 Professor, Department of Plant Biotechnology, Faculty of Agriculture, University of Guilan, Rasht, Iran.
3 Assistant Professor, Department of Plant Biotechnology, Faculty of Agriculture, University of Guilan, Rasht, Iran.
4 Assistant Professor, Department of Cell and Molecular Biology, Faculty of Biological Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
چکیده [English]

Low temperature is an important abiotic stress limiting the production and geographical dispersion of many crops, including rapeseed, as an important oil crop. In this study, known cis-elements regulating molecular responses of plant to cold stress were used to identify genes involved in cold tolerance. From 62,384 Unigenes from Brassica Genome Gateway, 56 cold responsive genes were identified. Promoter analysis, gene ontology enrichment, co-occurrence, protein- protein interaction and in silico gene expression analysis were performed to validate the results of gene identification. The results showed known cis-element appearance in promoter region of all identified genes which involved in different biological pathways such as Calvin cycle, respiration and signal transduction in different cell parts. Co-occurrence study of identified genes illustrated mutual connections of genes with correlations above 0.64. Promoter analysis, PPI network and investigating transcription factors involved in transcription regulation of 56 identified genes and 98 co-expressed genes indicated the molecular mechanisms and similar pathways of plant response to cold and introduce candidate genes to be used in breeding and genetic engineering programs.

کلیدواژه‌ها [English]

  • Co-expressed regulatory network
  • Gene Ontology
  • Promoter analysis
  • Protein-protein interaction
  • Transcription factors

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