پیوندهای مفید
اخبار و اعلانات
آمار
| تعداد نشریات | 41 |
| تعداد شماره‌ها | 1,129 |
| تعداد مقالات | 9,667 |
| تعداد مشاهده مقاله | 17,602,235 |
| تعداد دریافت فایل اصل مقاله | 12,289,455 |
شناسایی و آنالیز پروموتر ژن‌های کلیدی دخیل در تحمل به تنش خشکی در مرحله زایشی جو با استفاه از آنالیز داده های ریزآرایه | ||
| فصلنامه علمی زیست فناوری گیاهان زراعی | ||
| دوره 9، شماره 3 - شماره پیاپی 29، خرداد 1399، صفحه 67-79 اصل مقاله (1.02 M) | ||
| نوع مقاله: علمی پژوهشی | ||
| شناسه دیجیتال (DOI): 10.30473/cb.2020.52899.1806 | ||
| نویسندگان | ||
| سیده مهری جوادی1؛ زهرا سادات شبر* 2؛ آسا ابراهیمی3؛ مریم شهبازی4 | ||
| 1گروه بیوتکنولوژی و اصلاح نباتات، واحد علوم و تحقیقات تهران، دانشگاه آزاد اسلامی، تهران، ایران | ||
| 2گروه پژوهشی زیست شناسی سیستم‌ها، پژوهشگاه بیوتکنولوژی کشاورزی، سازمان تحقیقات، آموزش و ترویج کشاورزی | ||
| 3گروه بیوتکنولوژی و اصلاح نباتات، علوم تحقیقات تهران، دانشگاه آزاد اسلامی، تهران، ایران | ||
| 4دانشیار فیزیولوژی گیاهی، دانشگاه علوم کشاورزی و منابع طبیعی گرگان، گرگان، ایران | ||
| چکیده | ||
| خشکی مهم‌ترین تنش محیطی است که باعث کاهش عملکرد محصولات گیاهی می‌شود. تحقیقات در راستای ایجاد ارقام متحمل به تنش خشکی از اهمیت فوق العاده‌ای برخوردار است. در این تحقیق تلاش شده است تا با آنالیز داده‌های تولید شده از طریق فناوری ریزآرایه، ژن‌های مهم پاسخگو به تنش خشکی و ژن‌های هاب در مرحله زایشی جو شناسایی‌شده و آنالیز پروموتور انجام گیرد. به همین منظور با استفاده از نرم‌افزار FlexArray تمامی ژن‌های دارای بیان افتراقی 5/2 ≥ و 5/2- ≥ در بین دو سری از آزمایشات ریزآرایه انجام شده در جو شناسایی شدند. نتیجه این تجزیه و تحلیل، شناسایی 559 ژن پاسخ‌دهنده به تنش خشکی در مرحله زایشی بود. ژن‌های هاب با استفاده از سه الگوریتم محاسباتی Cyto-Hubba در نرم-افزار Cytoscape مشخص شدند. این امر منجر به شناسایی 10 ژن غیر تکراری شد که به‌عنوان مؤثرترین ژن‌ها در پاسخ به تنش خشکی در نظر گرفته شدند. براساس بررسی هستی‌شناسی ژن‌های دارای بیان افتراقی و ژن‌های هاب، تنظیم رونویسی از گروه‌های اصلی بود که نشان دهنده اهمیت عوامل رونویسی در مکانیسم تحمل به خشکی می‌باشد. در میان عوامل رونویسی می‌توان به HvCBF6، HvDRF1.3، LFL1، VP1، WRKY71 و ABI5 (متعلق به خانواده‌های AP2، WRKY و bZIP) اشاره کرد. آنالیز پرموتر نشان داد که برخی از خانواده‌های عوامل رونویسی از جمله AP2، AT-hook family، bHLH، NAC، bZIP و MYB قابلیت اتصال به 85 درصد از پرموترهای شناسایی‌شده را دارند. مطالعه این عوامل رونویسی، می‌تواند به شناخت هر چه بیشتر سازوکار تحمل به تنش خشکی در جو کمک کند. | ||
| کلیدواژه‌ها | ||
| جو؛ تنش خشکی؛ ژن هاب؛ آنالیز پروموتر؛ هستی شناسی | ||
| موضوعات | ||
| ژنتیک مولکولی و مهندسی ژنتیک | ||
| عنوان مقاله [English] | ||
| Identification and promoter analysis of the key drought tolerance involved genes in reproductive stage in barley using microarray data analysis. | ||
| نویسندگان [English] | ||
| Seyede mehri Javadi1؛ Zahra-Sadat Shobbar2؛ Asa Ebrahimi3؛ Maryam Shahbazi4 | ||
| 1Department of Biotechnology and Plant Breeding, Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran | ||
| 2Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Education and Extension Organization (AREEO) | ||
| 3Department of Biotechnology and Plant Breeding, Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran | ||
| 4Associate Professor, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran | ||
| چکیده [English] | ||
| Drought is the most important environmental stress that reduces crop yield. Therefore, research toward developing tolerant varieties is of great importance. In this study, microarray data analysis was used for identification of drought stress responsive genes and relevant hub genes in the reproductive stage of barley, and then their promoter analysis was performed. To achieve the goal, all the differentially expressed genes (DEGs) at drought conditions with fold changes ≥+2.5 and ≤-2.5 were identified between two microarray data-series in barley using FlexArray software. Bioinformatics analysis indicated that 559 genes were drought responsive at reproductive stage. The hub genes were distinguished using three Cyto-Hubba computational algorithms by Cytoscape software. Based on the hub analysis results, 10 unique (non-redundant) genes were identified as the most effective genes in response to drought stress. According to the gene ontology analysis of DEGs and hub genes, regulation of transcription were among the major groups indicating the importance of transcription factors (TFs) at drought tolerance mechanism. Amongst the hubs, several TFs such as HvCBF6, HvDRF1.3, LFL1, VP1, ABI5 and WRKY71 genes (belonged to AP2, WRKY and bZIP families) were observed. Promoter analysis was also revealed that some TF families including AP2, AT-hook family, bHLH, NAC, bZIP and MYB had binding site in 85% of promoters of the drought responsive genes and the hub genes in barley. Studying these transcription factors can help in better identification of drought tolerance mechanism in barley. | ||
| کلیدواژه‌ها [English] | ||
| Barley (Hordeum vulgare), drought stress, hub gene, gene ontology, promoter analysis | ||
| مراجع | ||
|
Abebe T , Melmaiee K, Berg V, Wise R (2010) Drought response in the spikes of barley: gene expression in the lemma, palea, awn, and seed. Funct Integr Genomics 10: 191–205.
Agrawala, S, Barlow M, Cullen H and Lyon B (2001). The drought andhumanitariancrisis incentral and south west Asia :a climate perspective.International Research Institute for ClimatePrediction,IRI Special Report,20:1-11.
Ahmed I, Huaxin D, Weite Zh, Fangbin C, Guoping Zh, Dongfa S and Feibo W (2013) Genotypic differences in physiological characteristics in the tolerance to drought and salinity combined stress between Tibetan wild and cultivated barley. Plant Physiol Biochem 63: 49-60.
Alghabari F, Muhammad Z (2018) Effects of drought stress on growth, grain filling duration, yield and quality attributes of barley (Hordeum vulgare L.). Bangl J Bot 47: 421-428.
Altschul SF, GishW, MillerW, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol Mol. 215(3): 403-410.
Altschul SF, Madden TL, Schäffer A A, Zhang J, Zhang Z, Miller W, Lipman D J(1997) Gapped BLASTand PSI-BLAST: a new generation of protein database search programs .Nucleic Acids Res. 25 (17):3389-3402.
Amini, R.(2013). Drought stress tolerance of barley (Hordeum vulgare L.) affected by priming with PEG. Intl J Farm & Alli Sci. 2(20): 803-808.
Arriagada O, Freddy M, Yerko Q , Alejandro D (2017) Identification of QTL underlying agronomic, morphological and physiological traits in barley under rainfed conditions using SNP markers. Acta Scientiarum. Agronomy 39: 321-329.
Budak H, Kantar M, Yucebilgili Kurtoglu K (2013) Drought tolerance in modernand wild wheat. TSWJ. 16.
Cartharius K, Kornelie F, Korbinian G, Bernward K, Manuela H, Andreas K, Matthias FM , and Thomas W(2005) MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 21: 2933-2942.
Castells E, Casacuberta JM (2007) Signalling through kinase-defective domains: the prevalence of atypical receptor-like kinases in plants. J. Exp. Bot. 58(13): 3503-3511.
Chen WJ, Zhu T (2004) Networks of transcription factors with roles in environmental stress response. Trends Plant Sci. 9:591-596.
Food and Agriculater Organization (2014) FAO 2014 [WWW document]. http://faostat3.fao.org.
Fowler S, Michael FT (2002) Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14: 1675-1690.
Freeling M, Shabarinath S (2009) Conserved noncoding sequences (CNSs) in higher plants. Curr Opin Plant Biol 12: 126-132.
Gao SQ, Chen M, Xu ZS, Zhao CP, Li L, Xu HJ, Tang YM, Zhao X, Ma YZ (2011). The soybean GmbZIP1 transcription factor enhances multiple abiotic stress tolerances in transgenic plants. Plant Mol. Biol 75: 537-553.
Guo P, Michael B, Stefania G, Salvatore C, Guihua B, Ronghua L, Maria V, Rajeev K V, Andreas G, Jan V (2009) Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage. J Exp Bot 60: 3531-3544.
Hackenberg M, Perry G, Peter L and BuJun Sh, (2015) Differential expression of micro RNA s and other small RNA s in barley between water and drought conditions. Plant Biotech J 13: 2-13.
Hu H, Mingqiu D, Jialing Y, Benze X, Xianghua L, Qifa Zh and Lizhong X (2006) Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc Natl Acad Sci U S A 103: 12987-12992.
Hübner S, Abraham BK and Karl JS (2015) RNA-Seq analysis identifies genes associated with differential reproductive success under drought-stress in accessions of wild barley Hordeum spontaneum. BMC Plant Biol 15: 134.
Janiak A, Kwasniewski M, Sowa M, Gajek K, Żmuda K, Kościelniak J and Szarejko I (2018) No Time to Waste: Transcriptome Study Reveals that Drought Tolerance in Barley May Be Attributed to Stressed-Like Expression Patterns that Exist before the Occurrence of Stress. Front. Plant Sci. 8:2212.
Li S, Fu Q, Huang W, Yu D (2009) Functional analysis of an Arabidopsis transcription factor WRKY25 in heat stress. Plant Cell Rep. 28: 683-693.
Liang J, Xin Ch, Guangbing D, Zhifen P, Haili Zhang, Q, Kaijun Y, Hai L and Maoqun Y(2017) Dehydration induced transcriptomic responses in two Tibetan hulless barley (Hordeum vulgare var. nudum) accessions distinguished by drought tolerance. BMC genomics 18: 775.
Li J, Besseau S, Toronen P, Sipari N, Kollist H, Holm L, Palva ET (2013) bbDefense related transcription factors WRKY70 and WRKY54 modulate osmotic stress tolerance by regulating stomatalaperture in Arabidopsis. New. Phytol. 200: 457-472.
Mingyu Z, Zhengbin Z, Shouyi C, Jinsong Z, Hongbo S (2012) WRKY transcription factor superfamily: structure, origin and functions. AJB. 11: 8051-8059.
Mir R, Mainassara Zh, Nese S, Richard T and Rajeev K (2012) Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops. Theor Appl Genet 125: 625-645.
Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2012) AP2/ERFfamily transcription factors in planta biotic stress responses. Biochim. Biophys. Acta. 1819: 86-96.
Mohanta TK, Mohanta N, Mohanta YK, Parida P, Bae H (2015) Genome-wide identification of Calcineurin B-Like (CBL) gene family of plants reveals novel conserved motifs and evolutionary aspects in calcium signaling events. BMC Plant Biol. 15(1): 9-18.
Morran S, Eini O, Pyvovarenko T, Parent B, Singh R, Ismagul A, Eliby S, Shirley N, Langridge P, Lopato S (2011) Improvement of stress tolerance of wheat and barley by modulation of expression of DREB/CBF factors. Plant Biotechnol. J. 9: 230-249.
Nakashima K, Yamaguchi-Shinozaki K, Shinozaki K (2014) Thetranscriptional regulatory network in the drought response and its crosstalk in abiotic stress responses including drought, cold, and heat. Front. PlantSci. 5:170.
Ozturk Z, Neslihan T, Deyholos Ml, Michalowski Ch, Galbraith D, Gozukirmizi N, Tuberosa R and Bohnert H (2002) Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley. Plant Mol. Biol. 48: 551-573.
Rashid M, Guangyuan H, Guangxiao Y, Hussain J and Xu, Y (2012) AP2/ERF transcription factorin rice: genome-wide can vas and syntenic Relationships between monocots and eudicots. Evol. Bioinform.Online. 8: 321.
Rushton PJ, Somssich IE, Ringler P ,Shen QJ (2010) WRKY transcription factors. Trends Plant Sci. 15: 247-258.
Shao H, Chu L, Jaleel CA, Zhao C (2008) Water-deficit stress-induced anatomical changes in higher plants. Comptes Rendus Biologies. 331(3): 215-225.
Sharoni AM, NuruzzamanM, Satoh K, Shimizu T, Kondoh H, Sasaya T et al (2011) Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice. Plant Cell Physiol. 52: 344-360.
Shinozaki K, Dennis ES (2003) Cell signalling and gene regulation: global analyses of signal transduction and gene expression profiles. Curr. Opin. Plant Biol. 6: 405-409.
Singh A, Giri J, Kapoor S, Tyagi AK, Pandey GK (2010) Protein phosphatase complement in rice: genome-wide identification and transcriptional analysis under abiotic stress conditions and reproductive development. BMC Genomics 11(1): 435.
Skubacz A, Daszkowska-Golec Aand Szarejko I (2016) The Roleand Regulation of ABI5 (ABA-Insensitive 5) in Plant Development, Abiotic StressResponses and Phytohormone Crosstalk. Front. Plant Sci. 7:1884.
Smoot ME, Keiichiro O, Johannes R, Peng-Liang W and Trey I, 2011. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431-432.
Song X, Li Y, Hou X (2013) Genome-wideanalysis of the AP2/ERF Transcription factors upper family in Chines ecabbage (Brassicarapa ssp. pekinensis). BMCGenomics 14:573.
Szklarczyk D, Andrea F, Stefan W, Kristoffer F, Davide H, Jaime HC, Milan S, Alexander R, Alberto S and Kalliopi PT (2014) STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Res.
Talamè V, Neslihan Z, Hans J, Roberto T(2006) Barley transcript profiles under dehydration shock and drought stress treatments: a comparative analysis. J Exp Bot 58: 229-240.
Tian T, Yue L, Hengyu Y, Qi Y, Xin Y, Zhou D, Wenying X and Zhen S (2017) agriGO v2. 0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Res. 45: 122-129.
Tran L, Keiichi M (2010) Functional genomics of soybean for improvement of productivity in adverse conditions. Funct Integr Genomics 10: 447-462.
Umezawa T, Miki F, Yasunari F, Kazuko Y and Kazuo Sh (2006) Engineering drought tolerance in plants: discovering and tailoring genes to unlock the future. Curr Opin Biotechnol 17: 113-122.
Wang, N., Xu, S., Sun, Y. et al (2019) The cotton WRKY transcription factor (GhWRKY33) reduces transgenic Arabidopsis resistance to drought stress. Sci Rep. 9: 724.
Wang X,Zeng J, Li Y, Rong X, Sun J, Sun T, Li M, Wang L, Feng Y, Chai R, Chen M, Chang J, Li K, Yang Gand He G (2015) Expression of TaWRKY44 wheat WRKY gene ,in transgenic tobacco confers multiple abiotic stress tolerances. Front. PlantSci. 6: 615.
Wani SH, Singh NB, Devi TR, Haribhushan A, Jeberson SM, Malik C P (2013) Engineering abiotic stress tolerance in plants:extricating regulatory gene complex in Conventional and Non-Conventional Interventions in Crop Improvement, eds C.P. Malik, G.S. Sanghera and S.H. Wani (New Delhi: CABI), 1-19.
Worch S, Rajesh K, Harshavardhan V, Pietsch Ch, Korzun V, Kuntze L, Börner A, Wobus U, Röder M, Sreenivasulu N (2011) Haplotyping, linkage mapping and expression analysis of barley genes regulated by terminal drought stress influencing seed quality. BMC Plant Biol 11:1.
Yamaguchi-Shinozaki K, Shinozaki K (2005) Organization of cis-acting regulatory elements in osmotic-and cold-stress-responsive promoters. Trends Plant Sci. 10: 88-94.
Zhang X, Xiaohong L, Wenzhi W, Tingjun Zh, Xiaomin Z, Guobao X, Guoju W and Huhu K (2018) Spatiotemporal variability of drought in the northern part of northeast China. HYDROL PROCESS 32: 1449-1460.
Zheng J, Junjie F, Mingyue G, Junling H, Yunjun L, Min J, Quansheng H, Xiying G, Zhigang D and Hongzhi W (2010) Genome-wide transcriptome analysis of two maize inbred lines under drought stress. Plant Mol. Biol 72: 407-421.
Zlatev Zlatko, C. L. F. (2012) An overview on drought induced changes in plant growth, water relations and photosynthesis." Emir. J. Food Agric: 24(1): 57-72. | ||
|
آمار تعداد مشاهده مقاله: 776 تعداد دریافت فایل اصل مقاله: 667 |
||