با همکاری مشترک دانشگاه پیام نور و انجمن بیوتکنولوژی جمهوری اسلامی ایران

نوع مقاله : علمی پژوهشی

نویسندگان

1 کارشناسی‌ارشد بیوتکنولوژی کشاورزی، دانشگاه پیام نور، تهران

2 دانشیار گروه بیوتکنولوژی، دانشکده کشاورزی، دانشگاه صنعتی اصفهان

چکیده

خشکی یکی از عمده‌ترین تنش‌های محیطی محسوب می‌شود که رشد و توسعه گیاهان را تا حد زیادی تحت تاثیر قرار می‌دهد. واکنش‌های گیاهان در برابر این تنش‌ با بروز تغییرات زیاد در شبکه‌های پیچیده حاوی تعداد زیادی ژن همراه است. در پژوهش حاضر تغییرات الگوی بیان ژن‌ها در دو ژنوتیپ حساس و متحمل گیاه برنج (به‌عنوان گیاه C3) و گیاه ذرت (به‌عنوان گیاه C4) با استفاده از آرایه‌های ژنوم ذرت شامل 734/ 17پروب‌ست و ژنوم برنج شامل 381/57 پروب‌ست مورد بررسی قرار گرفت. داده‌های ریزآرایه‌، جهت شناسایی ژن‌های درگیر در پاسخ به تنش در دو شرایط کنترل و تنش از بانک اطلاعاتی GEO/NCBI، گرفته شد. نتایج نشان داد که به ترتیب تعداد 1861 (49/10 درصد) و 1753 (8/9 درصد) ژن در ژنوتیپ حساس و متحمل ذرت و تعداد 9252 (16 درصد) و 7971 (8/13 درصد) ژن در ژنوتیپ حساس و متحمل برنج پس از تنش خشکی در سطح یک درصد تغییر بیان معنی‌داری داشتند. از این تعداد به ترتیب 1012 و 175 ژن در برگ ژنوتیپ متحمل و حساس برنج و ذرت افزایش بیان معنی‌داری نشان دادند. دیاگرام ون نشان داد که به ترتیب تعداد 663 و 158 ژن به ترتیب و به صورت مشترک در ارقام متحمل و حساس برنج و همچنین ذرت کاهش بیان معنی‌داری دارند. گیاه برنج (به‌عنوان گیاه C3) پنج برابر در مقایسه با گیاه ذرت (به‌عنوان گیاه C4) واکنش گسترده‌تری به تنش خشکی از خود نشان داد. گروه‌بندی کارکردی ژن‌های دارای افزایش بیان در دو گونه گیاهی مشخص کرد که در ذرت گروه کارکردی پروتئین‌های ریبوزومی و ‌فسفاتازها دارای بیشترین تعداد ژن هستند در حالیکه در برنج گروهای کارکردی اتصال به فلزات، پاسخ به تنش، پاسخ به محرک‌های زیستی و انتقال پیام بیشترین ژن‌ها را شامل شدند.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

The Study of Functional Groups and Changes in Genes Expression Pattern of Rice (C3) and Maize (C4) under Drought Stress using Microarray Data Analysis

نویسندگان [English]

  • ِSedigheh Akhtartavan 1
  • Majid Talebi 2

1 Department of Agricultural Biotechnology, Payame Noor University, Tehran, Iran

2 Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.

چکیده [English]

Drought is one of the major environmental stresses that greatly affects growth and development of plants. The plants reaction against this stress is associated with showing massive changes in complex gene networks. In the present study, the changes of gene expression patterns in two sensitive and tolerant genotypes of rice (as C3 plant) and maize (as C4 plant) were investigated using maize genome arrays containing 17,734 probe sets and the rice genome containing 57/381 probe set. The microarray data were taken from the GEO/NCBI database on both stress and control conditions to identify the genes involved in responses to the stress. The results indicated that 1861 (10.49%) and 1753 (8.9%) genes in the sensitive and tolerant maize, respectively, and 9252 (16%) and 7971 (13.8%) genes in the sensitive and tolerant rice, respectively, changed significantly after drought stress at the level of one percent. From of these genes, 1012 and 175 genes in the sensitive and tolerant genotype leaf of rice and maize, were significantly up-regulated, respectively. The Venn diagram showed that 663 genes of rice and 158 genes of maize, have significantly down-regulated. Rice plant, as a C3 plant, showed five times wider reaction to drought stress in compared with maize plant, as a C4 plant. The functional grouping of the up-regulated genes in two species revealed that functional group of ribosomal proteins and phosphatases in maize plant have the most abundant categories, whereas the functional groups of metal-binding, stress response, response to biological stimuli and signals in rice plant contained the highest percentage of the genes.

کلیدواژه‌ها [English]

  • Drought stress
  • Zea mays
  • Oryza sativa
  • Microarray analysis
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT (2000) Gene Ontology: tool for the unification of biology. Nat. Genet. 25: 25-29.
 Bögre L, Ligterink W, Heberle-bors E, Hirt H (1996) Mechanosensors in plants. Nat. 383: 489-490.
Bohnert HJ, Nelson DE, Jensen RG (1995) Adaptations to environmental stresses. Plant Cell. 7: 1099-1111.
Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 19: 185-193.
Bray EA (1993) Molecular responses to water deficit. Plant Physiol. 103: 1035-1040.
Chang C, Stewart RC (1998) The two-component system regulation of diverse signaling pathways in prokaryotes and eukaryotes. Plant Physiol. 117: 723-731.
Chaves MM (1991) Effects of Water Deficits on Carbon Assimilation. J. Exp. Bot. 42: 1-16.
 Chaves MM, Perira J (1992( Water stress, CO2, and climate change. J. Exp. Bot. 43: 1131-1139.
Chaves MM, Maroco JP, Pereira JS )2003( Understanding plant responses to drought from genes to the whole plant. Funct. Plant Biol. 30: 239-264.
Craita B, Gerats T (2013) Plant tolerance to high temperature in a changing environment: scientific fundamentals and production of heat stress-tolerant crops. Front Plant Sci.4: 273.
Degenkolbe T, Do PT, Zuther E, Repsilber D, Walther D, Hincha DK, Koehl KI (2009) Expression profiling of rice cultivars differing in their tolerance to long-term drought stress. Plant Mol. Biol. 69: 133-153.
Edwards GE, Ku MSB (1987) Biochemistry of C3-Cintermediates. In: Hatch M.D, Boardman NK (eds), Biochemistry of Plants: Photosynthesis. London: Academic Press. 10: 275-325.
Epstein HE, Lauenroth WK, Burke IC, Coffin DP )1998( Regional productivities of plant species in the Great Plains of the United States. Plant Ecol. 134: 173-195.
Gallie DR, Caldwell C, Pitto L (1995) Heat Shock Disrupts Cap and Poly (A) Tail Function during Translation and Increases mRNA Stability of Introduced Reporter mRNA. Plant Physiol. 108: 1703-1713.
Hasegawa PM, Bressan RA, Zhu JK, Bohnert HJ )2000( Plant cellular and molecular responses to high salinity. Ann. Rev. Plant Physiol. Plant Mol. Biol. 51: 463-499.
Heidarvand L, Maali Amiri R (2010) What Happens in Plant Molecular Responses to Cold Stress? Acta Physiol. Plant. 32: 419-431.
Hura T, Hura K, Grzesiak M (2007) Effect of Long-term Drought Stress on Leaf Gas Exchange and Fluorescence Parameters in C3 and C4 Plants. Acta Physiol. Plant. 29: 103-113.
Ichimura K, Mizoguchi T, Yoshida R, Yuasa T, Shinozaki K (2000) Various abiotic stresses rapidly activate Arabidopsis MAP kinases ATMPK4 and ATMPK6. Plant J. 24: 655-65.
Ingram J, Bartels D (1996) The molecular basis of dehydration tolerance in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47: 377-403.
Inoue T, Higuchi M, Hashimoto Y, Seki M, Kobayashi M, Kato T, Tabata S, Shinozaki K, Kakimoto T (2001) Identification of CRE1 as a cytokinin receptor from Arabidopsis. Nat. 22: 1060-1073.
Irizarry Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 4: 249-64.
Javadi S, Shapar ZS, Pourabed E, Ghadiri S (2015) Reconstruction of gene networks involved in response to drought stress in the leaves tissue of barley. Available at http: //biotechcongress.ir/, Tehran, Iran.
Jonak C, Kiegeri S, Ligterink W, Barker PJ, Huskisson NS, Hirt H (1996) Stress signaling in plants: a mitogen-activated by cold and drought. Proc. Natl. Acad. Sci. 20: 11274-11279.
Kerk D, Bulgrien J, Smith DW, Barsam B, Veretnik S, Gribskov M (2002) The complement of protein phosphatase catalytic subunits encoded in the genome of Arabidopsis. Plant Physiol. 129: 908-25.
Kopka J, Pical C, Gray JE, Muller-Rober B (1998) Molecular and enzymatic characterization of three phosphoinositide-specific phospholipase C isoforms from potato. Plant Physiol. 116: 239-50.
Kotak S, Larkindale J, Lee Ung, Koskull-Do¨ ring P.von, Vierling E, Scharf KD (2007) Complexity of the heat stress response in plants. Curr. Opin. Plant Biol.10: 310-316.
Krishna P, Gloor G (2001) The Hsp90 faily of proteins in Arabidopsis thaliana. Cell Stress Chaperones 6: 238-246.
Lee BH, Henderson DA, Zhu JK )2005( The Arabidopsis cold-responsive transcriptome and its regulation by ICE1. Plant Cell. 17:3155-3175.
Maclean JL, Hettle GP (Eds) (2002). Rice almanac: Source book for the most important economic activity on earth. 3rd Ed. Int. Rice Res. Inst. CABI. pp 253.
Moon J-C, Yim WC, Lim SD, Song K, Lee B-M (2014) Differentially expressed genes and in silico analysis in response to ozone (O3) stress of soybean leaves. Aust. J. Crop Sci. 8: 276-283.
Mott IW, Wang RRC )2007( Comparative transcriptome analysis of salt-tolerant wheat germplasmlines using wheat genome arrays. Plant Sci.173: 327–339.
Munnik T, Meijer HJ, Ter Riet B, Hirt H, Frank W, Bartels D, Musgrave A (2000) Hyperosmotic stress stimulates phospholipase D activity and elevates the levels of phosphatidic acid and diacylglycerol pyrophosphate. Plant J. 22: 147-54.
Mustilli A-C, Merlot S, Vavasseur A, Fenzi F, Giraudat J (2002) Arabidopsis OST1 protein kinase mediates the regulation of stomatal aperture by abscisic acid and acts upstream of reactive oxygen species production. Plant Cell. 14: 3089–3099.
Nakashima K, Ito Y, Yamaguchi-Shinozaki K (2009) Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses. Plant Physiol. 149: 88-95.
Nayyar H (2003) Accumulation of osmolytes and osmotic adjustment in water-stressed wheat (Triticum aestivum) and maize (Zea mays) as affected by calcium and its antagonists. Environ. J. Exp. Bot. 50: 253-264.
Nelson DM, Sheng Hu F, Tian J, Stefanova I, Brown TA (2004) Response of C3 and C4 plants to middle-Holocene climatic variation near the prairie-forest ecotone of Minnesota. Proc. Natl. Acad. Sci. U.S.A. 13: 562-567.
Neves SR, Ram PT, Iyengar R )2002( G protein pathways. Science. 296: 1636-9.
Nocter G, Gomez L, Vanacker H, Foyer CH (2002) Interactions between biosynthesis, compartmentation and transport in the control of glutathione homeostasis and signaling. J. Exp. Bot. 53: 1283-1304.
Osakabe K, Shinozaki S, Tran LS.P, (2014) Response of plants to water stress. Front. Plant Sci. 5: 86.
Pierce M, Raschke K, (1980) Correlation between loss of turgor and accumulation of abscisic acid in detached leaves. Planta. 148: 174-18.
Raghavendra AS, Gonugunta VK, Christmann A, Grill E (2010) ABA perception and signaling. Trends Plant Sci. 15: 395-401.
Rock C (2000) Pathways to abscisic acid-regulated gene expression. New Phytol. 148: 357-396.
Sangwan V, Orvar BL, Beyerly J, Hirt H, Dhindsa RS (2002) Opposite changes in membrane fluidity mimic cold and heat stress activation of distinct plant MAP kinase pathways. Plant J. 31: 629-638.
Shi Y, Mosser DD, Morimoto RI (1998) Molecular chaperones as HSF1-specific transcriptional repressors .Genes Dev. 12: 654–666.
Shinozaki K, Yamaguchi-Shinozaki K (1997) Gene expression and signal transduction in water-stress response. Plant Physiol. 115: 327–334.
Shinozaki K, Yamaguchi-Shinozaki K (1999) In molecular responses to cold, drought, heat and salt stress in higher plants. Science. pp 170.
Shinozaki K, Yamaguchi-Shinozaki K, Seki M (2003) Regulatory network of gene expression in the drought and cold stress responses. Curr. Opin. Plant Biol. 6: 410-417.
Shinozaki K, Yamagachi–Shinozaki. K (2007) Gene networks involved in drought stress response and tolerance. J. Exp. Bot. 58: 221-227.
Simpson S D, Nakashima K, Narusakam Y, Seki M, Shinozaki K, Yamaguchi- Shinozaki K (2003) Two different novel cis-acting elements of erd1, a clpA homologous Arabidopsis gene function in induction by dehydration stress and dark-induced senescence Plant J. 33: 259-270.
Taheri H, Alizade H, Naghavi MR, Seafi AR (2004) MAPKs expression pattern under drought stress in bread wheat. Trends Biochem. Sci. 22: 172-176.
Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker SI, Mandal J, Xu J, Cui X, Close TJ (2005) Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol. 139: 822-835.
Ward JK, Tissue DT, Thomas RB, Strain BR (1999) Comparative responses of model C3 and C4 plants to drought in low and elevated Co2. Global Change Biol. 5: 857-867.
Wurgler-Murphy SM, Saito S (1997) Two-component signal transducers and MAPK cascades. Trends Biochem. Sci. 22: 172-176.
Xiong L, Schumaker KS, Zhu JK )2002( Cell signaling during cold, drought, and salt stress. Plant Cell. 14: 165-183.
Zali H, Taverani MR, Salemian J, Aulad J, Bastami-nejhad S (2013) The network for the analysis of gene expression microarray data of DNA. J. Med. Sci. 20: 150-138.
Zheng J, Fu J, Gou M, Huai J, Liu Y, Jian M, Huang Q, Guo X, Dong Z, Wang H, Wang G (2010) Genome-wide transcriptome analysis of two maize inbred lines under drought stress. Plant Mol. Biol.72: 407-421.