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Identification of key genes involved in heat stress response in Brassica napus L.: reconstruction of gene networks, hub genes, and promoter analysis | ||
Iranian Journal of Genetics and Plant Breeding | ||
دوره 11، شماره 1 - شماره پیاپی 21، مرداد 2022، صفحه 71-86 اصل مقاله (1.51 M) | ||
نوع مقاله: Research paper | ||
شناسه دیجیتال (DOI): 10.30479/ijgpb.2023.18795.1340 | ||
نویسندگان | ||
Nina Makvandi1؛ Abozar Ghorbani* 2؛ Mahsa Rostami2؛ Atefe Rostami3؛ Ali Akbar Ghasemi-Soloklui2 | ||
1Department of Agricultural Biotechnology, Payame Noor University (PNU), Isfahan, Iran. | ||
2Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran. | ||
3Department of Biology, Faculty of Science, University of Zanjan, Zanjan, Iran. | ||
تاریخ دریافت: 28 اردیبهشت 1402، تاریخ بازنگری: 29 تیر 1402، تاریخ پذیرش: 15 مرداد 1402 | ||
چکیده | ||
Brassica napus is a versatile crop with oil and protein-rich seeds, used in food, industry, medicine, and animal feed. However, heat stress limits its productivity, making it essential to identify genes and pathways involved in stress response. We analyzed differentially expressed genes (DEGs) in B. napus under heat stress using bioinformatics tools to identify key genes and pathways. Firstly, DEGs were analyzed for gene interactions using the STRING database and visualized using Cytoscape. To identify key genes involved in heat stress response in B. napus L., we employed the CytoHubba tool for hub gene identification. Additionally, we conducted Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses to gain insights into the functional roles and potential biological pathways associated with these genes. We also used MEME Suite to analyze the promoter regions of hub genes. Our results showed decreased activity of the b6-f complex, a key component of the electron transport chain, under heat stress. We also identified significantly enriched calcium transporter ATPase and heat shock protein family (HSP20). KEGG and cluster analyses highlighted the importance of membrane lipids, galactose metabolism, and protein processing in the endoplasmic reticulum in stress and signal transduction. Our study provided key genes, including transcription factors and chaperones for developing heat-resistant plants via genetic modification. However, these promising results were obtained through rigorous bioinformatics analysis and require further validation using experimental approaches, such as gene editing, phenotypic characterization, and field trials. | ||
کلیدواژهها | ||
Biological networks؛ Brassica napus؛ Heat stress؛ Hub genes؛ Promoter analysis؛ Protein-protein interactions | ||
عنوان مقاله [English] | ||
شناسایی ژنهای کلیدی درگیر در پاسخ به تنش گرمایی در Brassica napus L.: بازسازی شبکههای ژنی، ژنهای هاب و تجزیه و تحلیل پروموترها | ||
نویسندگان [English] | ||
مینا مکوندی1؛ ابوذر قربانی2؛ مهسا رستمی2؛ عاطفه رستمی3؛ علی اکبر قاسمی سلوکلویی2 | ||
1گروه بیوتکنولوژی کشاورزی، دانشگاه پیام نور (PNU)، اصفهان، ایران. | ||
2دانشکده تحقیقات کشاورزی هسته ای، پژوهشکده علوم و فناوری هسته ای (NSTRI)، کرج، ایران. | ||
3گروه زیست شناسی، دانشکده علوم، دانشگاه زنجان، زنجان، ایران. | ||
چکیده [English] | ||
Brassica napus محصولی با دانه های روغنی غنی از پروتئین است که در غذا، صنعت، دارو و خوراک دام استفاده می شود. استرس گرمایی بهره وری آن را محدود می کند و شناسایی ژن ها و مسیرهای دخیل در پاسخ به استرس را ضروری می کند. ما ژنهای با بیان متفاوت را در B. napus تحت تنش گرمایی، تحلیل کردیم. آن ها برای تعاملات ژنی با استفاده از پایگاه داده STRING تحلیل شدند و با استفاده از Cytoscape مشاهده شدند. برای شناسایی ژنهای کلیدی درگیر در پاسخ استرس گرمایی در از ابزار CytoHubba برای شناسایی ژن هاب استفاده کردیم. علاوه بر این، هستی شناسی ژن و مسیرهای مهمی که در آن دخیل هستند را تحلیل نمودیم تا بینشی در مورد نقش عملکردی و مسیرهای بیولوژیکی مرتبط با این ژن ها به دست آوریم. همچنین از MEME Suite برای تحلیل نواحی پروموتر ژن های هاب استفاده کردیم. نتایج کاهش فعالیت کمپلکس b6-f، یک جزء کلیدی از زنجیره انتقال الکترون، تحت تنش گرمایی را نشان داد و ATPase ناقل کلسیم غنی شده و خانواده پروتئینی تنش حرارتی را شناسایی کردیم. تحلیل های KEGG و خوشه بندی، اهمیت لیپیدهای غشایی، متابولیسم گالاکتوز و پردازش پروتئین در شبکه آندوپلاسمی را در تنش و انتقال سیگنال برجسته کردند. مطالعه ما ژنهای کلیدی، از جمله فاکتورهای رونویسی و چاپرونها را برای رشد گیاهان مقاوم در برابر حرارت از طریق اصلاح ژنتیکی ارائه کرد. این نتایج از طریق تحلیل بیوانفورماتیکی به دست آمده و نیاز به اعتبار سنجی بیشتر با استفاده از رویکردهای تجربی دارد. | ||
کلیدواژهها [English] | ||
شبکه های بیولوژیکی, Brassica napus, استرس گرمایی, ژن هاب, تجزیه و تحلیل پروموتر, برهمکنش های پروتئین-پروتئین | ||
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