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Metabolic Profiling for Identification of Potential Biomarkers in Potato Tuber Extracts Associated with Tolerance to Spongospora Subterranea F

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Metabolic Profiling for Identification of Potential Biomarkers in Potato Tuber Extracts Associated with Tolerance to Spongospora Subterranea F Metabolic profiling for identification of potential biomarkers in potato tuber extracts associated with tolerance to Spongospora subterranea f. sp. subterranea infection. By Gontse Kehumile Joyce Modisane Submitted in partial fulfilment of the requirements for the degree Magister Scientiae (M.Sc.) (Specialisation in Biochemistry) In the Faculty of Natural and Agricultural Sciences Department of Biochemistry, Genetics and Microbiology University of Pretoria South Africa Supervisor: Prof Z. Apostolides Co-supervisor: Prof J. van der Waals June 2019 SUBMISSION DECLARATION I, Gontse Kehumile Joyce Modisane declare that the thesis/dissertation, which I hereby submit for the degree at Magister Scientiae (Specialisation in Biochemistry) the University of Pretoria, is my work and has not previously been submitted by me for the degree at this or any other tertiary institution. Signature: Date: i PLAGIARISM DECLARATION Full name: Gontse Kehumile Joyce Modisane Student number: 15056237 Title of the work: Metabolic profiling for identification of potential biomarkers in potato tuber extracts associated with tolerance to Spongospora subterranea f. sp. subterranea infection. Declaration 1. I understand what plagiarism entails and am aware of the University’s policy in this regard. 2. I declare that this Dissertation is my own original work. Where someone else’s work was used (either from a printed source, internet or any other source), due acknowledgement was given, and reference was made according to departmental requirements. 3. I did not make use of another student’s previous work and submit it as my own. 4. I did not allow and will not allow anyone to copy my work with the intention of presenting it as his or her own work. Signature: Date: ii DEDICATION This research is dedicated to my pillar, the queen of my heart, my mother Helen Modisane, who always supported me throughout my studies and my life. I wouldn’t have made it without your caring, love and guidance. I love u mom. iii ACKNOWLEDGEMENTS Firstly and foremost, I would like to thank my creator, God the Father, for giving me life and strength for accomplishing my dreams to become a research scientist. Without Him, I wouldn’t have made it. I would like to express my heartfelt appreciation and gratitude to my supervisor Professor Zeno Apostolides, for your professional courtesy in supervising me. And particularly for giving me this opportunity to learn and for all the mentorships you have provided me throughout the three years of master’s journey. You have been a good father to me. To my project leader, Professor Jacquie van der Waals, thanks for being part of this potato project and providing us with potato samples. Without these plants, this MSc project wouldn’t have been possible. I also would like to express my gratitude to my funders, National Research Foundation (NRF) scholarship and Potatoes South Africa bursary for their financial support. To my beloved family, my son, Ronewa Phenyo Modisane, thank you for coming into my life during my Masters. You are such a blessing. My two sisters, Mrs Beverley Kgame and Miss Kgomotso Modisane, and my one and only brother, Mr Abram Modisane thanks for your support and love. And to the most important person in my life, my mother Helen Modisane, I gratefully dedicate this work to you, and I would like to thank you for your moral support and for believing in me. Even when I lost hope, you have always pushed me to work hard. To my partner in crime, my husband, to be, the father of my child, Mr Robert Mashau, thank you for your caring, loving and support. Even when it was too much, you always offered a shoulder to cry on. To my friends and colleagues, Miss Moleboheng Lekota and Miss Lettilia Xhakaza, I would like to express my thanks for their support and assistance through my research work. Thank you for being there for me through thick and thin. I pray that may the Almighty God protect you as He provides all your heart desires, and may your life be filled with success. There is no doubt that without the motivation, guidance and support of these people I wouldn’t have completed this Master’s degree, God bless them all. iv PREFACE The research set out in this thesis was carried out to search for metabolic biomarkers in potato tuber extracts associated with tolerance to Spongospora subterranea f. sp. subterranea infection using UPLC-QTOF/MS-based untargeted metabolomics in combination with chemometrics methods. The thesis chapters’ start with the introduction (Chapter 1), followed by the experimental work (Chapter 2), results (Chapter 3) and discussion (Chapter 4). The overall findings of the study have been summarized in a conclusion (Chapter 5) and lastly followed by limitations of the study and future perspectives (Chapters 6 and 7). Symposia The content of this dissertation was presented at the following Symposia: Oral presentation at Biochemistry symposium, held at University of Pretoria (Groenkloof campus) which took place on 27 September 2017. Presentation by G.K.J Modisane, M. Lekota, J. van der Waals and Z. Apostolides, Metabolic profiling for identification of potential biomarkers in potato tuber extracts associated with tolerance to Spongospora subterranea f. sp. subterranea infection. Poster presentation at Potatoes South Africa research symposium, held at Khaya Ibhubesi conference centre (Parys) which took place on 24-27 July 2018. Presentation by G.K.J Modisane, M. Lekota, J. van der Waals and Z. Apostolides, Metabolic profiling for identification of potential in potato tuber extracts associated with tolerance to Spongospora subterranea f. sp. subterranea infection. Poster presentation at Department of Biochemistry, Genetics and Microbiology (BGM) research symposium, held at Future Africa UP Campus (Hatfield) which took place on 06 December 2018. Presentation by G.K.J Modisane, M. Lekota, J. van der Waals and Z. Apostolides, Metabolic profiling for identification of potential biomarkers in potato tuber extracts associated with tolerance to Spongospora subterranea f. sp. subterranea infection. v TABLE OF CONTENTS SUBMISSION DECLARATION ......................................................................................................... i PLAGIARISM DECLARATION ........................................................................................................ ii DEDICATION...................................................................................................................................... iii ACKNOWLEDGEMENTS ................................................................................................................ iv PREFACE .............................................................................................................................................. v LIST OF FIGURES ............................................................................................................................. ix LIST OF APPENDICES ...................................................................................................................... x LIST OF ABBREVIATIONS ............................................................................................................. xi SUMMARY .........................................................................................................................................xiv CHAPTER 1: INTRODUCTION ........................................................................................................ 1 1.1. The host ...................................................................................................................................... 1 1.1.1. Phytochemicals in potatoes ................................................................................................. 1 1.1.1.1. Phenolic compounds ................................................................................................... 2 1.1.1.2. Carotenoids ................................................................................................................. 4 1.1.1.3. Steroidal glycoalkaloids .............................................................................................. 5 1.1.1.4. Terpenoids ................................................................................................................... 6 1.1.2. Health benefits of potato ..................................................................................................... 8 1.2. The pathogen ............................................................................................................................. 9 1.2.1. Pathogen occurrence, life cycle and epidemiology ............................................................. 9 1.2.2. Control measures of Spongospora subterranea f. sp. subterranea ................................... 13 1.2.3. Mechanism of resistance to Spongospora subterranea f .sp. subterranea ....................... 14 1.2.4. Detection and quantification of Spongospora subterranea f .sp. subterranea infection .. 14 1.3. Plant-pathogen interaction ..................................................................................................... 15 1.3.1. How plants respond to pathogen attacks ........................................................................... 17 1.3.2. Metabolomics analysis of plant-pathogen interactions ..................................................... 19 1.4. Metabolomics ........................................................................................................................... 22 1.4.1. What is metabolomics?
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