مدل‌سازی شبکه ژنی و تنظیمی الگوهای رونوشتی در القای سامانه دفاعی کلزا در برابر ‏Sclerotinia sclerotiorum

نوع مقاله : علمی پژوهشی

نویسندگان

1 استادیار، گروه مهندسی تولید و ژنتیک گیاهی، دانشکده کشاورزی، دانشگاه علوم کشاورزی و منابع طبیعی خوزستان. ملاثانی. ایران.

2 دانشیار، گروه گیاه پزشکی، دانشکده کشاورزی، دانشگاه علوم کشاورزی و منابع طبیعی خوزستان. ملاثانی. ایران.

چکیده

پوسیدگی ساقه اسکلروتینیایی (SSR) که توسط قارچ خاکزاد Sclerotinia sclerotiorum ایجاد می‌شود، علاوه بر کاهش 10-20 درصدی عملکرد محصول، منجر به کاهش کیفیت بذر در کلزا (Brassica napus) می‌شود. عامل مهار زیستی Pseudomonas chlororaphis PA23 قادر است با القاء مقاومت سیستمیک، گیاه کلزا را از اثرات مخرب قارچ همی‌بیوتروف S. sclerotiorum مصون نگه دارد. با این حال سازوکار ملکولی القای مقاومت در برابر این بیمارگر تا حدود زیادی ناشناخته است. از این رو در مطالعه حاضر، الگوهای رونوشتی در گیاه کلزا با استفاده از سیستم کنترل زیستی باکتری PA23 مورد بررسی قرار گرفت تا با بررسی شبکه‌های برهم‌کنش پروتئین-پروتئین (PPI) به‌ویژه تمرکز بر ژن‌های کلیدی (Hub genes) احتمالی، هستی‌ شناسی ژن‌ها (Gene Ontology)، مسیرهای بیوشیمیایی و بررسی شبکه‌های تنظیمی از طریق بررسی پروموتر ژن‌های کلیدی و پیش‌بینی miRNAها در برهم‌کنش گیاه-بیمارگر، به اطلاعات جامع‌تری از پاسخ گیاه کلزا پیش تیمار شده با PA23 در برابر آلودگی S. sclerotiorum رسید. با استفاده از الگوریتم‌های محاسباتی افزونه CytoHubba در نرم‌افزار Cytoscape، گره‌هایی (Nodes) با بیشترین درجه برهم‌کنشی با سایر ژن‌ها در شبکه ژنی تحت عنوان ژن‌های کلیدی شناسایی شدند که عمدتاً در حفظ و بازیابی مسیرهای متابولیکی و فعالیت فتوسنتزی، کنترل وضعیت اکسیداسیون/ احیای (redox) سلولی، بیوسنتز اسیدهای آمینه آروماتیک و هورمون‌های گیاهی، فعال‌سازی پیام‌‌رسان‌های دفاعی وابسته به MAPK، تنظیم اسیمیلاسیون سولفور و بیوسنتز سیستئین نقش داشتند. همچنین تحلیل خوشه‌بندی شبکه با استفاده از الگوریتم IPCA در افزونه Cytocluster، ماژول‌های عملکردی را که عمدتاً در بیوسنتز اسیدهای آمینه آروماتیک و تولید متابولیت‌های دفاعی در مسیر شیکیمات نقش داشتند را به عنوان مسیرهای اصلی پاسخ دفاعی حاصل از PA23 در برابر SSR معرفی کرد. آنالیز پروموتر ژن‌های کلیدی در ناحیه5′UTR ، عناصر تنظیمی سیس (CRE) متنوعی نظیر موتیف‌های وابسته به پیام‌رسان اکسین را در تنظیم پاسخ‌های دفاعی بر علیه آلودگی S. sclerotiorum شناسایی کرد. پیش‌بینی miRNAهایی که با ژن‌های کلیدی برهم‌کنش دارند، با استفاده از برنامه وب محور psRNATarget، miRNAهای متعلق به خانواده‌های miR172، miR395، miR6028، miR6029، miR6032، miR6035، miR166، miR156، miR396 و miR824 را به عنوان عناصر اصلی شبکه تنظیمی بیان ژن‌های کلیدی معرفی کرد. شناخت این برهم‌کنش‌ها در القای سامانه دفاعی کلزا در برابر آلودگی قارچی SSR می‌تواند به توسعه سیستم‌های کنترل بیولوژیکی جهت مدیریت بیماری‌های گیاهی و حفاظت از سیستم‌های زراعی کمک کند و مکانیسم‌های پایه جهت ایجاد واریته‌های متحمل به بیماری را توسعه دهد.

کلیدواژه‌ها

موضوعات


عنوان مقاله [English]

Gene and regulatory network modeling of transcriptomic patterns in defense priming of rapeseed against Sclerotinia sclerotiorum infection

نویسندگان [English]

  • Hengameh Taheri 1
  • Mohamad Hamed Ghodoum Parizi pour 2
1 Assistant Professor, Department of Plant Production and Genetics, Faculty of Agriculture, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Iran
2 2. Associate Prof, Department of Plant Protection, Faculty of Agriculture, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Iran.
چکیده [English]

Sclerotinia stem rot (SSR), caused by the soil-borne fungus Sclerotinia sclerotiorum, adversely impacts seed quality in rapeseed (Brassica napus) causing a 10-20% reduction in crop yield. The biological control agent Pseudomonas chlororaphis PA23 can protect rapeseed from the deleterious effects of the hemibiotrophic fungus S. sclerotiorum by inducing systemic resistance. However, little is known about the molecular mechanisms underlying defense priming and its regulatory processes. In this study, we amid to identify the protein-protein interaction (PPI) networks, with a particular focus on potential hub genes, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and regulatory network analysis including hub genes promoter analysis and miRNA prediction in canola plants pre-treated by PA23 in the presence of S. sclerotiorum using transcriptome data. Using the computational algorithms of the CytoHubba plugin in the Cytoscape platform, nodes with the highest interactions within the gene network were identified as hub genes, which are mainly involved in the maintenance and retrieval of metabolic pathways and photosynthetic activities, controlling cellular oxidation/reduction (redox) status, biosynthesis of aromatic amino acids and plant hormones, activation of MAPK-mediated defense signals, regulation of sulfur assimilation and cysteine biosynthesis. Using clustering analysis based on the IPCA algorithm in the Cytocluster plugin, functional modules effective in defense priming against SSR infection were identified. These modules were primarily involved in the biosynthesis of aromatic amino acids and the production of defensive metabolites in the shikimate pathway. The promoter analysis of 5′UTR region of hub genes identified various cis-regulatory elements (CREs), such as auxin signaling-responsive motifs involved in regulating defense responses against S. sclerotiorum infection. Prediction of miRNAs targeting hub genes, using the web-based psRNATarget program, revealed that miRNAs belonging to the families miR172, miR395, miR6028, miR6029, miR6032, miR6035, miR166, miR156, miR396 and miR824 play key roles as regulatory elements in the gene expression network of hub genes. These findings can aid in establishing biological control systems for plant disease management and protection of agricultural systems, as well as in advancing the fundamental mechanisms for developing disease-tolerant varieties.

کلیدواژه‌ها [English]

  • Biological control
  • microRNAs
  • protein interaction networks
  • RNA sequencing
  • Sclerotinia stem rot
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