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Molecular Analysis of Betula Papyrifera Populations from a Mining Reclaimed Region: Genetic And

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Molecular Analysis of Betula Papyrifera Populations from a Mining Reclaimed Region: Genetic And Molecular analysis of Betula papyrifera populations from a mining reclaimed region: genetic and transcriptome characterization of metal resistant and susceptible genotypes by Gabriel Theriault A thesis submitted in partial fulfillment of the requirements for the degree of Doctor (PhD) in Biomolecular Sciences The Faculty of Graduate Studies Laurentian University Sudbury, Ontario, Canada © Gabriel Theriault, 2017 THESIS DEFENCE COMMITTEE/COMITÉ DE SOUTENANCE DE THÈSE Laurentian Université/Université Laurentienne Faculty of Graduate Studies/Faculté des études supérieures Title of Thesis Titre de la thèse Molecular analysis of Betula papyrifera populations from a mining reclaimed region: genetic and transcriptome characterization of metal resistant and susceptible genotypes Name of Candidate Nom du candidat Theriault, Gabriel Degree Diplôme Doctor of Philosophy Department/Program Date of Defence Département/Programme Biomolecular Sciences Date de la soutenance March 14, 2017 APPROVED/APPROUVÉ Thesis Examiners/Examinateurs de thèse: Dr. Kabwe Nkongolo (Supervisor/Directeur(trice) de thèse) Dr. A. Omri (Committee member/Membre du comité) Dr. L Leduc (Committee member/Membre du comité) Approved for the Faculty of Graduate Studies Approuvé pour la Faculté des études supérieures Dr. David Lesbarrères Monsieur David Lesbarrères Dr. Thomas Hutchinson Dean, Faculty of Graduate Studies (External Examiner/Examinateur externe) Doyen, Faculté des études supérieures Dr. Peter Ryser (Internal Examiner/Examinateur interne) ACCESSIBILITY CLAUSE AND PERMISSION TO USE I, Gabriel Theriault, hereby grant to Laurentian University and/or its agents the non-exclusive license to archive and make accessible my thesis, dissertation, or project report in whole or in part in all forms of media, now or for the duration of my copyright ownership. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also reserve the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report. I further agree that permission for copying of this thesis in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their absence, by the Head of the Department in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that this copy is being made available in this form by the authority of the copyright owner solely for the purpose of private study and research and may not be copied or reproduced except as permitted by the copyright laws without written authority from the copyright owner. ii Abstract The objectives of the present study were to; 1) determine if there’s an association between plant population diversity and genetic variation in white birch (Betula papyrifera) populations with soil metal contamination in the Greater Sudbury region (GSR), 2) assess if metal contamination and soil liming has an effect on global DNA methylation, 3) develop and characterize the transcriptome of B. papyrifera under nickel stress and, 4) assess gene expression dynamics in white birch in response to nickel stress. No association between plant population diversity and genetic variation with metal contamination was found. Liming increases plant population diversity but has no effect on genetic variation in the studied white birch populations. There was a decrease in root cytosine methylation in metal-contaminated sites compared to references. Treatment with the dose corresponding to total level of Ni or Cu (1,600 mg/kg Ni, 1,312 mg/kg Cu or combined) in sites of the GSR generated different responses within segregating populations analyzed. The main Ni resistance mechanism of white birch was associated with the prevention of translocation of Ni from root to shoot. We also observed lower ZAT11 and glutathione reductase expression in resistant genotypes compared to susceptible. The transcriptome of B. papyrifera was developed for the first time using Next Generation Sequencing. RNA from Ni resistant, moderately-susceptible, susceptible and water controls treatment was sequenced. A total of 209,802 trinity genes were identified and were assembled to 278,264 total trinity transcripts. In total, 215,700 transcripts were annotated and compared to the published B. nana genome. Overall, a genomic match for 61% transcripts with the reference genome was found. Expression profiles were generated and 62,587 genes were found to be significantly differentially expressed among the nickel resistant, susceptible, and untreated libraries. The main nickel resistance mechanism in B. papyrifera is a downregulation of genes associated with translation and cell iii growth, and upregulation in genes involved in the plasma membrane. Seven candidate genes associated to nickel resistance were identified. They include Glutathione S-transferase, Thioredoxin, Putative transmembrane protein, Nramp transporter, TonB-like family protein and TonB-like dependent receptor. This TonB receptor was found to be exclusive to the Betula genus. Keywords White birch, Betula papyrifera, metal contamination, genetic variation, nickel resistance, transcriptome, gene expression, restoration, methylation, metal toxicity iv Acknowledgements I would like to thank my supervisor Dr. Kabwe Nkongolo for the support given to me throughout my years of doctoral studies. I would also like to extend my sincere gratitude to my committee members, Dr. Abdel Omri and Dr. Leo Leduc, my external reviewers, Dr. Hutchinson and Dr. Peter Ryser for taking the time to assess my thesis. In addition, I would like to say thank you to Dr. Peter Beckett and Dr. Graeme Spiers for the help with site identification and sample collection. To my fellow lab mates and family members I thank you for the support and help you have given me. Finally, I thank the Natural Sciences and Engineering Research Council of Canada for the financial support. v Table of contents Thesis defense committee .............................................................................................................. ii Abstract ......................................................................................................................................... iii Acknowledgements ......................................................................................................................... v Table of contents ............................................................................................................................ vi List of figures ............................................................................................................................... xiv List of tables .............................................................................................................................. xviii List of appendices ......................................................................................................................... xx Chapter 1: Literature review ........................................................................................................ 1 1.1. Soil pollution in terrestrial ecosystems .............................................................................. 1 1.1.1. Metal contamination in the Greater Sudbury region ...................................................... 1 1.1.2. Impact of the mining industry on soil chemistry............................................................ 2 1.1.3. Impact of the mining industry on terrestrial ecosystem health ...................................... 4 1.1.3.1. Plants ....................................................................................................................... 4 1.1.3.2. Humans and other vertebrates ................................................................................. 5 1.1.3.3. Invertebrates and microorganisms .......................................................................... 6 1.1.4. Emission reduction and the Sudbury Land Reclamation Program ................................ 6 1.1.5. Effects of liming on soil chemistry ................................................................................ 7 1.2. The genus Betula.................................................................................................................. 8 1.2.1. Betula papyrifera ............................................................................................................ 9 1.2.2. Effects of metal contamination and low soil pH on B. papyrifera ............................... 10 vi 1.3. Genetic variation ............................................................................................................... 12 1.3.1. Effects of metal contamination on genetic variation .................................................... 14 1.4. Molecular markers ............................................................................................................ 14 1.4.1. Restriction fragment length polymorphism (RFLP) .................................................... 15 1.4.2. PCR based methods ...................................................................................................... 15 1.4.2.1. Amplified fragment length polymorphism (AFLP) .............................................. 16 1.4.2.2. Random amplified polymorphic DNA (RAPD) ...................................................
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