Investigating the molecular underpinnings underlying morphology and changes in carbon partitioning during tension wood formation in Eucalyptus

Tension wood has distinct physical and chemical properties, including altered fibre properties, cell wall composition and ultrastructure. It serves as a good system for investigating the genetic regulation of secondary cell wall biosynthesis and wood formation. The reference genome sequence for Eucalyptus grandis allows investigation of the global transcriptional reprogramming that accompanies tension wood formation in this global wood fibre crop. We report the first comprehensive analysis of physicochemical wood property changes in tension wood of Eucalyptus measured in a hybrid (E. grandis 9 Eucalyptus urophylla) clone, as well as genome-wide gene expression changes in xylem tissues 3wk post-induction using RNA sequencing. We found that Eucalyptus tension wood in field-grown trees is characterized by an increase in cellulose, a reduction in lignin, xylose and mannose, and a marked increase in galactose. Gene expression profiling in tension wood-forming tissue showed corresponding down-regulation of monolignol biosynthetic genes, and differential expression of several carbohydrate active enzymes. We conclude that alterations of cell wall traits induced by tension wood formation in Eucalyptus are a consequence of a combination of down-regulation of lignin biosynthesis and hemicellulose remodelling, rather than the often proposed up-regulation of the cellulose biosynthetic pathway.South African Department of Science and Technology (DST), Sappi and Mondi, through the Forest Molecular Genetics Programme, the Technology and Human Resources for Industry Programme (THRIP, UID 80118) and the Bioinformatics and Functional Genomics Programme of the National Research Foundation (NRF, UID 18312) of South Africa.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1469-81372016-06-30hb201

Deep digital gene expression profiling during early and late tension wood induction in Eucalyptus trees

Genetic engineering of superior wood properties and exploiting natural genetic variation found within commercially important trees, such as Eucalyptus spp., promise to increase cellulose biomass production. It is therefore essential to understand the molecular genetics of wood formation. Digital Gene Expression (DGE) profiling is adept in not only assessing the expression level of genes transcriptome-wide, but also in characterising alternative splice forms of transcripts and identifying novel transcripts. Tension wood is a specialised type of wood which functions in the response to mechanical stress in trees and is formed on the upper side of a branch or a bent stem. The characteristics of tension wood differ from normal wood by increased cellulose and xyloglucan content and decreased lignin and xylan content. During tension wood formation, transcriptome-wide changes in the expression of genes involved in secondary cell wall formation underlie changes in cell wall composition. Most notably is an increase in fasciclin-like arabinogalactan protein (FLA) and xyloglucan endotransglucosylase (XTH) and a decrease in lignin biosynthesis gene expression. Differential expression patterns are shown by cellulose synthase (CesA) genes, which have been found to be either up- or down-regulated during tension wood formation. No previous study has profiled gene expression during early as well as late tension wood formation. The aim of this M.Sc study was to identify genes that are differentially expressed during early tension wood induction and late tension wood formation in the immature xylem tissues of Eucalyptus grandis x Eucalyptus urophylla hybrid trees. DGE profiling is a transcriptome-wide expression profiling technique based on ultra-high throughput second generation DNA sequencing technology. The processing, analysis and interpretation of DGE data has not yet been standardised. To address this problem, a case study was performed of DGE data mapping to seven well characterised Eucalyptus grandis CesA (EgCesA) genes. The DGE data processing guidelines developed based on this case study produced EgCesA expression profiles in normal wood that were comparable to the profiles of these genes determined with other technologies. A possible alternative splice variant occurring during tension wood formation was identified for the secondary cell wall gene EgCesA3. However future work is needed for the validation of this observation. Early tension wood induction and late tension wood formation was investigated by sampling differentiating xylem from ramets of a Eucalyptus grandis x Eucalyptus urophylla clone induced to form tension wood for 6 hours, 24 hours, 1 week, 2 weeks and 6 months. Up to 2,654 transcripts were found to be significantly differentially expressed during tension wood formation. FLA transcripts were the highest expressed transcripts and were, along with XTH genes, highly up-regulated in early and late tension wood formation. Genes differentially regulated during early tension wood formation reflected a general stress response and hormone signalling pathways. Late tension wood formation was marked by the differential regulation of secondary cell wall biosynthetic genes, which reflected the chemical composition of tension wood. Two secondary cell wall CesA genes were significantly up-regulated, while genes involved in lignin and xylan biosynthesis were significantly down-regulated. Observations suggest that the eucalypt trees used in this study formed tension wood to stabilise the bent stem, while apical dominance was transferred to new side branches which showed signs of extra secondary growth.Dissertation (MSc)--University of Pretoria, 2011.Geneticsunrestricte