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Doctoral thesis, 2015

Combined profiling in aspen

Obudulu, Ogonna

Abstract

This thesis presents efficient systems biology modelling strategies for integrating complex multi-platform datasets in order to increase our understanding of stress biology, wood formation and secondary cell wall formation in Populus trees and connected responses to perturbations in organisms, particularly aspen. It is based on studies reported in four appended papers, designated Papers I-IV. Paper I describes an enhanced framework for investigating and understanding multi-level oxidative stress responses and their influence on phenotypic variation in transgenic hipI-superoxide dismutase Populus plants. Paper II presents a modelling strategy based on a combination of Principal Component Analysis (PCA), Orthogonal Projections to Latent Structures (OPLS), and an enhanced stepwise linear modelling approach. This strategy revealed major transitions in the proteomes along the wood developmental series in Populus tremula (aspen) pinpointing, for example, the location of the cambial cell divisions leading to phloem and xylem cells, and the location of the secondary cell wall formation zone. A pairwise multivariate OPLS approach was applied in the study described in Paper III to analyse proteome dynamics during tension wood formation of Populus trees. Pairwise comparisons of four corresponding phases/tissue types in normal and tension wood formation allowed identification of several processes that were strongly enhanced and/or unique during tension wood formation. These multidisciplinary approaches together with a recently developed formulation of the OnPLS method was used in Paper IV to analyse a set of transgenic Populus trees carrying an RNAi construct for the Populus secretory carrier-associated membrane protein3 (PttSCAMP3) gene. Multilevel analysis of datasets from nine platforms (RNA sequencing, proteomic, metabolomic and wood chemical analyses) revealed a critical function for PttSCAMP proteins in wood formation and elucidated the underlying molecular mechanism. The systems biology approach presented in this thesis provides novel types of tools for elucidating stress responses and wood formation in Populus trees. Exploitation of very recent advances in multivariate methods such as OnPLS allowed the simultaneous combination of transcriptomic, proteomic and metabolomic data, as well as identification of differences and connections between the data sets, which would not have been possible using standard statistical methods.

Keywords

Systems biology; transcriptomics; proteomics; metabolomics; Populus; multivariate statistics; omics; wood development; aspen

Published in

Acta Universitatis Agriculturae Sueciae
2015, number: 2015:91
ISBN: 978-91-576-8380-9, eISBN: 978-91-576-8381-6
Publisher: Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences

Authors' information

Obudulu, Ogonna
Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology

UKÄ Subject classification

Forest Science
Wood Science

URI (permanent link to this page)

https://res.slu.se/id/publ/77480