آنالیز ترانسکریپتوم بافت برگ ارقام جو متفاوت در تشکیل زیست توده در مرحله زایشی

نوع مقاله: علمی پژوهشی

نویسندگان

1 دانشجوی دکتری، موسسه بیوشیمی و بیوتکنولوژی، دانشگاه هاله ویتنبرگ، هاله، آلمان.

2 استاد، بخش تغذیه ملکولی، دانشگاه هاله ویتنبرگ، هاله، آلمان

3 استاد، موسسه بیوشیمی و بیوتکنولوژی، دانشگاه هاله ویتنبرگ، هاله، آلمان.

4 استاد، بخش ریزازدیادی، موسسه گیاهان زینتی و سبزی صیفی، ایرفورت، آلمان

چکیده

کشف همبستگی میان تجمع زیست‌توده در گیاه و عملکرد، پیش نیاز درک ارتباط بین داده های امیکس و میزان رشد در گیاهان است. برای جستجوی این ارتباط بین ترانسکریپت‌ها و نقش تنظیمی آنها در تشکیل زیست‌توده لیگنوسلولزی در فاز زایشی جو، پروفایل ترانسکریپت‌ها دو هفته پس از گلدهی در 3 لاین جو بهاره مورد استفاده قرار گرفت. یک ریزآرایه سفارشی (custom microarray) متشکل از 56000 اولیگونوکلئوتید برای آنالیز ترانسکریپتوم برگ پرچم در مرحله زایشی استفاده شد. شبکه ی همبستگی ترانسکریپت‌های درگیر در متابولیسم ثانویه و متابولیسم RNA، دارای تعداد بیشتری همبستگی مثبت نسبت به منفی بود که از این بین یک سیگنال ملکول،ABH1-Cap binding protein بالاترین میزان اتصال را به دیگر ترانسکریپت‌ها نشان داد. آنالیز آماری یک همبستگی مثبت بین ABH1-Cap binding protein و یک ژن کلیدی مسیر فنیل پروپانویید، به نام Cinnamoyl-COA reductase نشان داد. تلفیق داده های بدست آمده پیشنهاد کننده ی این موضوع هستند که ژن (CCR) Cinnamoyl-COA reductase ممکن است بتوانند به‌عنوان بیومارکر برای مهندسی اصلاح زیست‌توده لیگنوسلولزی در فاز زایشی جو استفاده شود.

کلیدواژه‌ها

موضوعات


عنوان مقاله [English]

Transcriptome analysis of leaf tissue in contrasting lines of barley for biomass formation at the reproductive stage

نویسندگان [English]

  • Mohammad Reza Ghaffari 1
  • Nicolaus von Wirén 2
  • Klaus Humbeck 3
  • Phillip Franken 4
1 Ph.D. student, Institute for Biochemistry and Biotechnology, Martin Luther University of Halle-Wittenberg, Halle, Germany.
2 Molecular Plant Nutrition Group, Martin Luther University of Halle-Wittenberg, Halle, Germany
3 Institute for Biochemistry and Biotechnology, Martin Luther University of Halle-Wittenberg, Halle, Germany.
4 Department Plant Propagation, Leibniz Institute of Vegetable and Ornamental Crops, Erfurt, Germany
چکیده [English]

Deciphering of network correlation operating in the plant biomass accumulation and yield production is a pre-requisite for understanding the relationships between omics data and growth rate in plants. To investigate the relationship among transcripts and their regulation for lignocellulose biomass formation at the generative stage of barley, transcript profiling was applied on three contrasting spring barley lines two weeks after flowering. A custom barley cDNA Microarray (Agilent Technologies, Germany) containing 56000 barley oligonucleotides was used for transcriptome analysis on flag leaves of spring barley. The network correlation of transcripts involved in secondary and RNA metabolism revealed a higher number of positive than negative correlations of which a signal molecule, ABH1-Cap binding protein showed the highest node degree centrality. Statistical test showed a strong positive interrelation between ABH1-Cap binding protein and a key gene of phenylpropanoid pathway, Cinnamoyl-CoA reductase. The integrated data suggested Cinnamoyl-CoA reductase (CCR) might be used as putative biomarker for engineering of lignocellulose biomass improvement at the generative stage in barley.

کلیدواژه‌ها [English]

  • Plant biomass
  • Transcriptome analysis
  • Network correlation analysis
  • Barley
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the royal statistical society. J. R. Statist. Soc. B. 57: 289-300.

Cass CL, Peraldi A, Dowd P.F, Mottia Y, Santoro N, Karlen SD, Bukhman YV, Foster CE, Thrower N, Bruno LC (2015) Effects of phenylalanine ammonia lyase (PAL) knockdown on cell wall composition, biomass digestibility, and biotic and abiotic stress responses in Brachypodium. J. Exp. Bot. 60: 4317-4335.

Gray J, Caparrós-Ruiz D, Grotewold E (2012) Grass phenylpropanoids: regulate before using! Plant Sci. 184:112-120.

Heidecker B, Hare JM (2007) The use of transcriptomic biomarkers for personalized medicine. Heart Fai. Rev. 12: 1-11.

Hugouvieux V, Kwak J.M, Schroeder J.I (2001). An mRNA cap binding protein, ABH1, modulates early abscisic acid signal transduction in Arabidopsis. Cell. 106: 477-487.

Lacombe E, Hawkins S, Doorsselaere J, Piquemal J, Goffner D, Poeydomenge O, Boudet A.M, Grima‐Pettenati J (1997) Cinnamoyl CoA reductase, the first committed enzyme of the lignin branch biosynthetic pathway: cloning, expression and phylogenetic relationships. Plant J. 11: 429-441.

Leung J, and Giraudat J (1998) Abscisic acid signal transduction. Annu. Rev. Plant Biol. 49:199-222.

Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics. 21:3448-3449.

Meyer RC, Steinfath M, Lisec J, Becher M, Witucka-Wall H, Törjék O, Fiehn O, Eckardt Ä, Willmitzer L, Selbig J (2007) The metabolic signature related to high plant growth rate in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 104:4759-4764.

Naoumkina MA, Zhao Q, Gallego‐Giraldo L, Dai X, Zhao PX, Dixon RA (2010) Genome‐wide analysis of phenylpropanoid defence pathways. Mol. Plant. Pathol. 11:829-846.

Perlack RD, Eaton LM, Turhollow Jr, Langholtz AF, Brandt MH, Downing CC, Graham ME, Wright LE, Kavkewitz LL, Shamey AM (2011) US billion-ton update: biomass supply for a bioenergy and bioproducts industry.

Prashant S, Sunita, MS, Pramod S, Gupta RK, Kumar SA, Karumanchi SR, Rawal S, Kishor PK (2011) Down-regulation of Leucaena leucocephala cinnamoyl CoA reductase (LlCCR) gene induces significant changes in phenotype, soluble phenolic pools and lignin in transgenic tobacco. Plant Cell Reports. 30: 2215-2231.

Riedelsheimer C, Lisec J, Czedik-Eysenberg A, Sulpice R, Flis A, Grieder C, Altmann T, Stitt M, Willmitzer L, Melchinger AE (2011) Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize. Proc. Natl. Acad. Sci. U.S.A. 109:8872-8877.

Shakirova F, Allagulova CR, Maslennikova D, Klyuchnikova E, Avalbaev A, Bezrukova M (2016) Salicylic acid-induced protection against cadmium toxicity in wheat plants. Environ. Exper. Bot. 122: 19-28.

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome. Res. 13: 2498-2504.

Shinya T, Iwata E, Nakahama K, Fukuda Y, Hayashi K, Nanto K, Rosa AC, Kawaoka A (2016) Transcriptional Profiles of Hybrid Eucalyptus Genotypes with Contrasting Lignin Content Reveal That Monolignol Biosynthesis-related Genes Regulate Wood Composition. Front. Plant. Sci. 7: 443.

Sreenivasulu N, Usadel B, Winter A, Radchuk V, Scholz U, Stein N, Weschke W, Strickert M, Close TJ Stitt M (2008) Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools. Plant. Physiol.14: 1738-1758.

Sulpice R, Nikoloski Z, Tschoep H, Antonio C, Kleessen S, Larhlimi A, Selbig J, Ishihara H, Gibon Y, Fernie AR (2013) Impact of the carbon and nitrogen supply on relationships and connectivity between metabolism and biomass in a broad panel of Arabidopsis accessions. Plant physiol. 162: 347-363.

Sulpice R, Pyl ET, Ishihara H, Trenkamp S, Steinfath M, Witucka-Wall H, Gibon Y, Usadel B, Poree F, Piques MC (2009) Starch as a major integrator in the regulation of plant growth. Proc. Natl. Acad. Sci. U.S.A. 106:10348-10353.

Tamasloukht B, Lam MSJWQ, Martinez Y, Tozo K, Barbier O, Jourda C, Jauneau A, Borderies G, Balzergue S, Renou JP (2011) Characterization of a cinnamoyl-CoA reductase 1 (CCR1) mutant in maize: effects on lignification, fibre development, and global gene expression. J. Exp. Bot. 62: 3837-3848.

Wang H, Yang JH, Chen F, Torres-Jerez I, Tang Y, Wang M, Du Q, Cheng X, Wen J, Dixon R (2016) Transcriptome analysis of secondary cell wall development in Medicago truncatula. BMC Genomics 17:23.

Yonekura-Sakakibara K, Tohge T, Matsuda F, Nakabayashi R, Takayama H, Niida R, Watanabe-Takahashi, A., Inoue, E., and Saito, K. (2008). Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene–metabolite correlations in Arabidopsis. The Plant Cell 20: 2160-2176.

Yoon J, Choi H, An G (2015) Roles of lignin biosynthesis and regulatory genes in plant development. J. Integr. Plant Biol. 57: 902-912.

Zhao Q, Dixon RA (2011) Transcriptional networks for lignin biosynthesis: more complex than we thought? Trends Plant. Sci. 16: 227-233.

Zhong R, Morrison WH, Himmelsbach DS, Poole FL, Ye ZH (2000) Essential role of caffeoyl coenzyme A O-methyltransferase in lignin biosynthesis in woody poplar plants. Plant Physiol. 124: 563-578.