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Identification of Genes Influencing Wood Fibre Properties in Eucalyptus Nitens

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Identification of Genes Influencing Wood Fibre Properties in Eucalyptus Nitens Identification of genes influencing wood fibre properties in Eucalyptus nitens By Nahida Bhuiyan B. Sc Ag (Hons 1); Master of Horticulture Thesis submitted in total fulfillment of the requirements for the degree of Doctor of Philosophy School of Forest and Ecosystem Science The University of Melbourne May 2008 Abstract Eucalypts are a major forest resource globally and the area of eucalypt plantations for pulp and paper production is expanding rapidly in Australia. Consequently, there is an increasing need to breed eucalypts with improved wood properties. Since many high value wood traits are under strong genetic control, identification of DNA markers linked to these traits will have application in breeding programs. In recent years there has been a shift in marker strategy away from QTL mapping in pedigrees to association studies in unrelated populations. In the latter approach, single nucleotide polymorphisms (SNPs) in candidate genes are screened to identify SNPs that significantly associate with wood traits. Significant SNPs could be used for marker-assisted selection (MAS) in breeding programs. The objectives of this study were to identify candidate genes that may influence pulp yield in eucalypts and to identify SNP variants in those genes that associate with superior wood and pulp traits. Approximately 300 trees from a full-sib Eucalyptus nitens progeny derived from a wide intra specific cross were used for gene discovery. DNA microarrays containing ~5800 young xylem of cDNAs Eucalyptus grandis were screened with probes synthesised from RNA isolated from trees with either high or low pulp yield. Forty-six transcripts were differentially regulated, of which 27 were more abundant in high pulp trees and 19 were more abundant in low pulp trees. All differentially expressed cDNAs were partially sequenced and searched against existing gene databases. Six genes were selected as putative pulp yield candidate genes based on their significant similarity to genes with known function and were named EgrCesA3 (cellulose synthase), EgrNAM1 (NAM II family protein), EgrXET (xyloglucan endotransglycosylase), EgrGalk (galactokinase), EgrHB1 (class III homeodomain leucine zipper protein) and EgrZnf1 (C3HC4 type zinc finger protein). Real-Time PCR was carried out on selected genes to confirm the accuracy of the microarray results. Full length cDNAs were obtained for EgrCesA3, EgrHB1 and EgrZnf1 and the candidate genes were partially characterised. An additional candidate gene, the novel gene EgrPAAPA, was selected based on previous research due to its high expression in the cambium and its expression in eucalypt branches. EgrPAAPA was cloned by screening an E. grandis cDNA library and fully sequenced. The full length EgrPAAPA encodes a short 172 amino acid protein rich in alanine, glutamic acid and proline residues. The EgrPAAPA protein appears to be a hydroxyproline-rich glycoprotein (HRGP) and the repetitive ‘PAAPA’ motif suggests that it might play a structural role in cell wall development. Southern blot analysis revealed that E. grandis has a single copy of the EgrPAAPA gene and northern blot analysis revealed that EgrPAAPA is most strongly expressed in xylem tissues. Allelic variation in EnCesA3, EnNAM1, EnPAAPA and EnHB1 was examined by sequencing each gene in 16 to 24 unrelated E. nitens individuals. SNPs were identified by sequence analysis and patterns of nucleotide diversity, linkage disequilibrium and the selection of suitable polymorphisms were estimated. A moderate level of nucleotide diversity (θw = 0.0056 and π = 0.0039) was observed and linkage disequilibrium was generally low, extending only a few hundred base pairs in each gene. Negative selection has been operating in EnHB1. Selected TagSNPs from EnNAM1, EnHB1 and EnPAAPA were genotyped across 300 unrelated E. nitens trees which had been phenotyped for six III wood quality traits including pulp yield, cellulose, lignin, Klason lignin, microfibril angle (MFA) and density. Five highly significant genetic associations (p<0.01) were detected between several SNPs in EnHB1 and all wood quality traits except density. A significant association was also found between EnPAAPA and MFA (p<0.05). No significant associations were found with any of the EnNAM1 SNPs. The strong genetic associations between SNPs in EnHB1 and a range of wood traits is consistent with this gene’s known role as a transcription factor controlling vascular development. Validation of these associations in different populations will be necessary in order to confirm these results. Alternatively, QTL mapping can be performed in order to confirm whether QTL for wood property traits can be detected at the EnHB1 and EnPAAPA loci. IV Declaration The contents presented in this thesis are my original work by study and research except where reference is made. It has not been submitted previously for a degree at any other University. The thesis is less than 100,000 words in length, exclusive of tables, illustrations and bibliography. Nahida Bhuiyan May 2008 V Acknowledgements I would like to thank my supervisors Dr Simon Southerton, Dr Gerd Bossinger and Dr Gavin Moran for their constant help and encouragement throughout this work. I would like to thank especially Dr Southerton for his endless support and guidance throughout the duration of my study. It has been a great honour and pleasure to work under his supervision. I thank Dr Bossinger for his willingness to share valuable experiences with me especially in the literature review. I thank Dr Bala Thumma and Dr Shannon Dillon for their assistance with association genetics analysis. I thank Dr Colleen MacMillan and Dr Karen Fullard for helpful discussion and advice during early stages of my research work. I thank my lab colleagues Charlie Bell, Maureen Nolan for their help in the lab. I also thank Dr Gapare Washington for helping me SAS genetics analysis. Special big thank to Judith Wright, Forest Biosciences, Clayton for helping me to get the predicted pulp yield data using NIRA analysis. I would like to thank to Dr Bingyu Zhang for her contributing in amplification and sequencing of EnCesA3 gene. I am grateful to the University of Melbourne and CSIRO for providing me an APA (I) scholarship. The industry partner for Australian Research Council project was Sappi, and their financial support is appreciated. In particular I would like to thank Dr Arlene Bailey and Dr Terry Stanger for their involvement and support throughout this research. I also thank CSIRO for providing the lab and computer facilities required to conduct the research. I would like to thank IP Australia for their patience as I have completed my thesis. I thank my husband, Anamul Bhuiyan and my son Navid for their patience and cooperation during my research work. I would also like to thank my parents, my brother Habib Bhuiyan and my sisters: Silva and Elena for their encouragement and well wishes throughout the work. VI Table of Contents Abstract……………………………………………………………………………….......II Declaration……………………………………………………………………………......V Acknowledgements……………………………………………………………………...VI Table of Contents……………………………………………………………………….VII List of Tables…………………………………………………………………………….XI List of Figures…………………………………………………………………………..XII List of Abbreviations…………………………………………………………………..XIV Chapter 1 Literature-review 1.1 Introduction………………………………………………………….2 1.2 The genus Eucalyptus……………………………………………….3 1.3 Wood fibre traits…….……………………………………………....5 1.4 Identifying genes involved in wood formation……………………...6 1.5 Wood formation……………………………………………………..9 1.6 Cell wall development……………………………………………..12 1.6.1 Cellulose biosynthesis………………………………..….13 1.6.2 Hemicellulose biosynthesis………………………….......16 1.6.3 Lignin biosynthesis……………………………………...16 1.6.4 Cell wall proteins…………………………………..……19 1.7 Family-based DNA linkage mapping…………………………......20 1.8 Population-based association studies……………………………...21 1.9 Single Nucleotide Polymorphism (SNP) discovery and genotyping………………………………………………………....24 1.10 Summary………………………………………………………......27 Chapter 2 Discovery of candidate genes for pulp yield in Eucalyptus nitens 2.1 Introduction……………………………………………………......29 2.2 Materials and methods………………………………………….....31 2.2.1 Plant material…………………………………………………..31 VII 2.2.2 Wood sample preparation and pulp trait analysis……………...32 2.2.3 Microarray printing…………………………………………….33 2.2.4 RNA isolation………………………………………..................33 2.2.5 Probe preparation…………………………………………….....34 2.2.6 Array hybridization and washing……………………………….35 2.2.7 Scanning and data analysis……………………………………..37 2.2.8 Sequencing and phylogenetic analysis………………………....38 2.2.9 Real time RT- PCR analysis…………………………………....38 2.3 Results……………………………………………………………….41 2.3.1 Selected genes more active in high pulp yield progeny………...42 2.3.2 Selected genes less active in high pulp yield progeny………….44 2.3.3 Functional classification of selected pulp yield genes………….46 2.3.4 Functional groupings of selected pulp yield genes…………..…48 2.3.5 Candidate genes putatively affecting pulp yield………….…….49 2.3.6 Real-time PCR assays…………………………………………..50 2.3.7 Expression of control gene in real-time RT-PCR………………52 2.3.8 Standard transcript levels for quantitative PCR assays………... 53 2.3.9 Quantitative analysis of EgrCesA3, EgrHB1 and EgrNAM1 by real-time PCR………………………………….…54 2.3.10 Phylogenetic analysis……………………………………...........58 2.4. Discussion………………………………………………………….72 2.4.1 Gene discovery strategy………………………………………...72 2.4.2 Pulp yield candidate genes……………………………………...75 2.4.2.1 EgrCesA3…………………………………………………75
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