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Allelic Diversity in the CAD2 and LIM1 Lignin Biosynthetic Genes Of Allelic diversity in the CAD2 and LIM1 lignin biosynthetic genes of Eucalyptus grandis Hill ex Maiden and E. smithii R. T. Baker by Minique Hilda de Castro Submitted in partial fulfilment of the requirements for the degree Magister Scientiae In the Faculty of Natural and Agricultural Sciences Department of Genetics University of Pretoria Pretoria June 2006 Under the supervision of Dr. Alexander A. Myburg and Prof. Paulette Bloomer © University of Pretoria DECLARATION I, the undersigned, hereby declare that the dissertation submitted herewith for the degree M.Sc. to the University of Pretoria, contains my own independent work and has not been submitted for any degree at any other university. _________________ Minique H. de Castro June 2006 ii PREFACE Wood fibre derived from Eucalyptus tree species is widely used in the pulp and papermaking industry. Exceptional survival capabilities, adaptability and hybrid vigour has made it possible to plant commercial Eucalyptus tree species across a wide variety of sites in tropical and subtropical regions of the world. Despite more than a decade of molecular genetic research in Eucalyptus, limited resources are available for molecular studies of the co-evolution of structural and regulatory genes and the association of allelic diversity in these genes with desirable phenotypes. This can mainly be attributed to the limited amount of eucalypt genomic sequences currently available. With the recent improvement of sequencing technologies and the availability of efficient single nucleotide polymorphism (SNP) assays, assessment of allelic diversity in tree genomes will become feasible in the near future. The amount of nucleotide diversity contained in naturally diverse Eucalyptus tree populations will provide a rich source of polymorphisms that can be used in association genetic studies and eventually in tree improvement programmes. The aim of this M.Sc. study was to assay nucleotide and allelic diversity in two lignin biosynthetic genes of two Eucalyptus tree species and to develop SNP markers that can be used to tag alleles of these genes in populations of these two species. Chapter 1 of this dissertation provides a review of the current knowledge of genetic variability and molecular evolution of tree genes with emphasis on genes involved in the lignin biosynthetic pathway. The importance of Eucalyptus tree species is discussed with reference to the growth and pulping characteristics of the target species of this study, E. grandis Hill ex Maiden and E. smithii R. T. Baker. Additionally, the chapter briefly reviews recent findings in the study of nucleotide diversity in forest trees and discusses the potential use of gene-based markers such as SNPs in tree improvement. Structural and regulatory genes operating in the same biochemical pathway may exhibit different patterns of molecular evolution. The LIM-domain1 (LIM1) transcription factor iii Preface gene, which has been implicated in the transcriptional regulation of key lignin biosynthetic genes including that of cinnamyl alcohol dehydrogenase2 (CAD2), presented a unique opportunity to study the molecular evolution of a structural gene together with that of its transcriptional regulator. Chapter 2 of this dissertation describes the molecular isolation, cloning and characterisation of the LIM1 genes of E. grandis and E. smithii. In addition, the cloning and characterisation of promoter sequences and putative cis-acting sequence elements contained therein are reported in this chapter. Chapter 3 describes the results of a survey of molecular diversity in alleles of the CAD2 and LIM1 genes cloned from 20 E. grandis and 20 E. smithii individuals. Detailed patterns of nucleotide diversity, allelic diversity and linkage disequilibrium (LD) are provided together with an inventory of putative SNP sites in each gene. The SNP sites identified in Chapter 3 were used for the identification and development of haplotype tagging marker panels for each gene in each species. In Chapter 4 the development of these marker panels is described and their informativeness for the analysis of SNP haplotypic diversity in species-wide reference samples of E. grandis and E. smithii is discussed. The possible application and usefulness of the SNP marker sets for the genotyping of other Eucalyptus species is briefly discussed. The findings presented in this M.Sc. dissertation represent the outcomes of a study undertaken from March 2003 to June 2006 in the Department of Genetics, University of Pretoria, under the supervision of Dr. A. A. Myburg and Prof. P. Bloomer. Chapters 2, 3 and 4 have been prepared in the format of independent manuscripts that can be submitted to refereed journals. A certain degree of redundancy may therefore exist between the introductory sections of these chapters and Chapter 1. Although the chapters have been prepared in the format of journal manuscripts, more supporting data are included in the thesis chapters than would normally be included in a manuscript for a research journal. iv Preface Preliminary results of this study were presented in the form of poster presentations at national and international meetings: • De Castro MH, Bloomer P, and Myburg AA (2004) Allelic diversity in lignin biosynthetic genes of Eucalyptus tree species. South African Genetics Society Conference, April 4-7. Stellenbosch, South Africa. • De Castro MH, Bloomer P, Stanger TK, and Myburg AA (2005) Comparative analysis of SNP marker diversity in lignin biosynthetic genes of Eucalyptus grandis and Eucalyptus smithii. IUFRO Tree Biotechnology Conference, November 6-7. Pretoria, South Africa. v ACKNOWLEDGEMENTS I would like to express my gratitude to the following people, organisations and institutes for assisting me in the completion of this project: • To Dr. Zander Myburg, for his professional, thorough and insightful leadership of this project, for his unlimited patience and time management when dealing with his students and an additional thanks for the unbelievable self-discipline and endurance in the finalising steps of this project. • To Prof. Paulette Bloomer, for excellent advice, insights and the comprehensive reviewing of this dissertation. • To my family, parents, and specifically to my sister, Therese de Castro, for assistance and dedication in the laboratory. • To all my past and present colleagues in the Forest Molecular Genetics Laboratory: Elna Cowley, Adrene Laubscher, Dr. Yoseph Beyene, Dr. Solomon Fekybelu, Martin Ranik, Honghai Zhou, Kitt Payn, Nicky Creux, Frank Maleka, Michelle Victor, John Kemp, Luke Solomon, Marja O’Neill, Grant McNair, Alisa Postma, Mmoledi Mphalele, Joanne Bradfield, Tracey-Leigh Hatherell and Eshchar Mizrachi for forming an enjoyable and intellectually stimulating environment in which to conduct research. • To the members of the Molecular Ecology and Evolution Laboratory, for their valuable advice and insights; especially to Isa-Rita Russo, Carel Oosthuizen, Arrie Klopper and Dr. Wayne Delport. • To all additional research colleagues and friends met in the duration of this project, for their encouragements and support. Specifically to Vinet Coetzee for her assistance and support in the finalisation of this dissertation. • To the Genetics Department of the University of Pretoria and the Forestry and Agricultural Biotechnology Institute (FABI), for providing a sound academic environment. vi Acknowledgements • To the Sequencing facility at the University of Pretoria, Renate Zipfel, Gladys Shabangu, Mia Bolton, for fast and efficient service, dedication and valuable advice during the progress of this project. • To Sappi Forest Products, for supplying the plant materials used in this study, for kind and efficient support, as well as for funding contributions. Espesially to Mr. Terry Stanger for valuable advice and inputs. • To the National Research Foundation of South Africa (NRF), for funding of a grant holder-linked scholarship. • To The Human Resources and Technology for Industry Programme (THRIP), for financial support of the research. vii TABLE OF CONTENTS Declaration .........................................................................................................................ii Preface..............................................................................................................................iii Acknowledgements ...........................................................................................................vi Table of contents............................................................................................................. viii List of tables .....................................................................................................................xii List of figures................................................................................................................... xiii CHAPTER 1 ...................................................................................................................... 1 Literature Review .............................................................................................................. 1 1.1 Introduction .............................................................................................................. 2 1.2 Pulp and paper production ....................................................................................... 4 1.3 Wood and fibre formation......................................................................................... 6 1.3.1 Xylogenesis ......................................................................................................
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