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Cell wall chemotyping for functional genomics

applications of pyrolysis-gas chromatography / mass spectrometry

Gerber, Lorenz (2012). Cell wall chemotyping for functional genomics. Diss. (sammanfattning/summary) Umeå : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2012:59
ISBN 978-91-576-7706-8
[Doctoral thesis]

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Abstract

The interest in lignocellulose as a sustainable resource for energy and materials has fueled research on biotechnology applications in tree breeding to improve biomass production and wood properties. An important aspect of this research is the basic understanding of gene function in wood formation, where analysis of wood chemistry and wood structure is of utmost importance.
Current research strategies often involve large-scale screening of plant material, and therefore there is a need for rapid chemical characterisation and classification (chemotyping) of samples. Pyrolysis-Gas Chromatography/Mass Spectrometry (Py-GC/MS) provides a chemical fingerprint with more than hundred peaks representing each sample. Despite the fact that the technique is very informative, the wealth of data resulting from each sample has prohibited its use as a high–throughput method in large scale projects. For this reason, a novel application of Py-GC/MS was developed. An automated data processing pipeline was created and implemented, which together with a new simplified rule-set to analyse Py-GC/MS data overcame the bottleneck of time-consuming data handling. The added value of the method was demonstrated by fingerprinting and classifying the wood of 736 transgenic hybrid aspen (Populus tremula x tremuloides) trees representing 44 different genotypes. Among these genes were fructokinases (FRK1 and 2) and sucrose synthase (SUS) isoforms, both involved in primary carbon metabolism. A battery of chemotyping tools demonstrated that the downregulation of FRK resulted more specifically in a decrease in cellulose biosynthesis, whereas the repression of SUS affected the amount of all of the major wood polymers. It was further demonstrated that the wood of transgenic SUS trees was affected in structure and mechanical properties. In another study, it was shown that down-regulating a lignin biosynthetic gene, cinnamate 4-hydroxylase, resulted in a modified wood structure in hybrid aspen. Interestingly, the large reduction in lignin content resulted in only minor effects on the ultimate tensile strength of the wood. Finally, the battery of chemotyping tools was used in a study to show that the transcription factor MYB103 is required for ferrulate-5-hydroxylase (F5H) expression and S-lignin biosynthesis in Arabidopsis thaliana.

Authors/Creators:Gerber, Lorenz
Title:Cell wall chemotyping for functional genomics
Subtitle:applications of pyrolysis-gas chromatography / mass spectrometry
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :2012
Volume:2012:59
Number of Pages:69
Papers/manuscripts:
NumberReferences
I.Lorenz Gerber, Mattias Eliasson, Johan Trygg, Thomas Moritz, Björn Sundberg (2012). Multivariate curve resolution provides a high-throughput data processing pipeline for Pyrolysis-Gas Chromatography/Mass Spectrometry. Journal of Analytical and Applied Pyrolysis 95, 95–100.
II.Rui C. Pinto, Lorenz Gerber, Mattias Eliasson, Björn Sundberg, Johan Trygg (2012). Strategy for minimizing between-study variation of large scale phenotypic experiments using multivariate analysis. submitted
III.Lorenz Gerber, Bo Zhang, Melissa Roach, András Gorzsás, Manoj Kumar, Totte Niittylä, Ingo Burgert, Björn Sundberg (2012). Reduced sucrose synthase activity in developing wood of hybrid aspen limits carbon allocation to all main cell wall polymers and modifies wood structure. manuscript
IV.Melissa Roach, Lorenz Gerber, David Sandquist, András Gorzsás, Mattias Hedenström, Manoj Kumar, Marie-Caroline Steinhauser, Regina Feil, Geoffrey Daniel, Mark Stitt, Björn Sundberg, Totte Niittylä (2012). Fructokinase is required for carbon partitioning to cellulose in aspen wood. The Plant Journal 70(6), 967–977.
V.Ingela Bjurhager, Anne-Mari Olsson, Bo Zhang, Lorenz Gerber, Manoj Kumar, Lars A. Berglund, Ingo Burgert, Björn Sundberg, Lennart Salmén (2010). Ultrastructure and mechanical properties of Populus wood with reduced lignin content caused by transgenic down-regulation of cinnamate 4-hydroxylase. Biomacromolecules 11(9), 2359–65.
VI.David Öhman, Brecht Demendts, Manoj Kumar, Lorenz Gerber, András Gorzsás, Geert Goeminne, Mattias Hedenström, Brian Ellis, Wout Boerjan, Björn Sundberg (2012). MYB103 promotes FERULATE-5-HYDROXYLASE expression and syringyl lignin biosynthesis in Arabidopsis stems. submitted
Place of Publication:Umeå
Publisher:Institutionen för skoglig genetik och växtfysiologi, Sveriges lantbruksuniversitet
ISBN for printed version:978-91-576-7706-8
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:F Plant production > F62 Plant physiology - Growth and development
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 104 Chemical Sciences > Analytical Chemistry
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Bioinformatics and Systems Biology (methods development to be 10203)
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Plant Biotechnology
Agrovoc terms:populus, cell walls, pyrolysis, lignification, lignocellulose, arabidopsis thaliana
Keywords:aspen, populus, cell wall analysis, analytical pyrolysis, wood formation, lignocellulose
URN:NBN:urn:nbn:se:slu:epsilon-e-587
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-587
ID Code:8994
Faculty:S - Faculty of Forest Sciences
Department:(S) > Dept. of Forest Genetics and Plant Physiology
External funders:FORMAS
Deposited By: Mr Lorenz Gerber
Deposited On:27 Aug 2012 13:56
Metadata Last Modified:02 Dec 2014 10:51

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