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Thesis Submitted for the Degree of Doctor of Philosophy University of Bath Department of Biology and Biochemistry September, 2017

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Thesis Submitted for the Degree of Doctor of Philosophy University of Bath Department of Biology and Biochemistry September, 2017 University of Bath PHD The Role of Interconversion of Scopoletin and Scopolin in Cassava Postharvest Physiological Deterioration (PPD) Fathoni, Ahmad Award date: 2017 Awarding institution: University of Bath Link to publication Alternative formats If you require this document in an alternative format, please contact: [email protected] General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 04. Oct. 2021 The Role of Interconversion of Scopoletin and Scopolin in Cassava Postharvest Physiological Deterioration (PPD) 1 The Role of Interconversion of Scopoletin and Scopolin in Cassava Postharvest Physiological Deterioration (PPD) Ahmad Fathoni A thesis submitted for the degree of Doctor of Philosophy University of Bath Department of Biology and Biochemistry September, 2017 Copyright Attention is drawn to the fact that copyright of this thesis rests with the author. A copy of this thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and they must not copy it or use material from it except as permitted by law or with the consent of the author. This thesis may be made available for consultation within the University Library and may be photocopied or lent to other libraries for the purposes of consultation. Signed………………………………….. Date…………………………….. Ahmad Fathoni i Acknowledgments All praise is due to God Almighty, Allah SWT, who has been giving me the strength and blessing throughout my life and research so that I am able to complete my PhD at Bath. I am very thankful to my mother, brothers and sisters, Angelina, Evelina and Erick for their endless love, support and prayers all the time. I would like to acknowledge the Ministry of Research and Technology and Higher Education (Kemenristekdikti), the Republic of Indonesia for the full financial support via Research and Innovation in Science and Technology Project (RISET-Pro) scholarship and Research Centre (RC) for Biotechnology-Indonesian Institute of Sciences (LIPI) for giving me the opportunity to pursue my PhD at the University of Bath. My gratitude goes to Prof. Dr. Enny Sudarmonowati, currently as Chairman of Deputy for Life Sciences, LIPI for her great support, and encouragement throughout my research career and also Dr. N. Sri Hartati, currently as Head of Plant Molecular Genetics and Biosynthetic Pathway Alteration Laboratory, RC for Biotechnology-LIPI for her support, and help. I am extremely grateful to my supervisors; Dr. John R. Beeching for his exemplary help, support, and guidance before and since I first came to Bath until I completed my thesis and Prof. Rod Scott for his best support during my study. I would like to acknowledge our collaborator from ETH, Zurich; Prof. Wilhelm Gruissem and Dr. Herve Vanderschuren for allowing me to do cassava transformation in their laboratory from May to June 2015, Dr. Ima Zainuddin for helping me through the transformation work, as well as everyone in Plant Biotechnology Lab, ETH, Zurich. I would like to thank Biochemical Society, and Departmental Travel Bursary for the travel grant, the Organizing committee for giving me partial fellowship to attend the 1st World Congress on Root and Tuber Crops (WCRTC) in China, January 2016. Again, I thank Biochemical Society for the second travel grant that had helped me to attend the International Conference on Root and Tuber ii Crops for Food Sustainability at the University of Brawijaya, Malang, Indonesia in October 2017. I would like to express my gratitude to Dr. James Doughty as the Director of Postgraduate Studies (Research), Dr. John R. Beeching and Prof. Rod Scott as the Head of Department for giving me such a great opportunity to write a proposal of the Global Challenges Research Fund (GCRF) Foundation Award for Global Agricultural and Food Systems Research to BBSRC in September 2016. I am greatly thankful to Mr. Andy Howman, the Head of International Student Recruitment, University of Bath and his team, for their tremendous help with several issues in the beginning of my study. I am most thankful to my colleagues, Dr. Shi Liu for his generous help and discussion, Dr. M.A.A. Wahab for helping me through difficult situations in the early stage of my PhD and all lab members of 4S/1.52 for their warm welcome. I thank Dr. Lidia Alhalaseh for providing me with standard scopolin and also Dr. Shaun Reeksting, Instrument Specialist, Faculty of Science for helping me with the biochemical analysis. I would like to thank Dr. Baoxiu Qi, Dr. Yaxiao Li, Dr. Ludi Wang, Dr. Julia Tratt and all lab members of 3S/1.13 for their kind help and discussion on Arabidopsis work. I would like to take this opportunity to express my thankfulness to all staff in the Department of Biology and Biochemistry, particularly teaching lab and glasshouse technician for their help. Thanks to Dr. M. Nor Hidayat, Remigius H. Wirawan and his family for tremendous help, all Indonesian students in Bath, my colleagues at LIPI and everyone who contributed to my research, and life in Bath over the last four years. iii This thesis is dedicated to my mother and my beloved one, Angelina. iv Table of Contents Acknowledgments...................................................................................... ii Table of Contents ...................................................................................... v List of Figures ........................................................................................... xi List of Tables ......................................................................................... xvii List of Abbreviations ............................................................................... xix Abstract ................................................................................................. xxii Chapter 1. Introduction and Literature Review ...........................................1 1.1. Introduction .........................................................................................2 1.1.1. Background of the thesis ..............................................................2 1.1.2. Aim of the thesis ...........................................................................5 1.1.3. Research strategies ......................................................................5 1.2. Cassava (Manihot esculenta Crantz) ..................................................6 1.2.1. Introduction ...................................................................................6 1.2.2. Taxonomy and morphology ..........................................................7 1.2.3. The origins and domestication ......................................................9 1.2.4. Importance of cassava as a crop ................................................11 1.2.5. Production and its challenges .....................................................12 1.3. Postharvest Physiological Deterioration (PPD) in cassava ................15 1.3.1. Introduction .................................................................................15 1.3.2. Physiological and biochemical responses during PPD ................17 1.3.3. Economic impact of PPD ............................................................29 1.3.4. Factors affecting PPD .................................................................30 1.3.5. Strategies to tackle PPD .............................................................31 1.4. Phenylpropanoid metabolism in higher plants ...................................35 1.5. Biosynthesis of scopoletin in cassava and its role on PPD ................37 1.6. Wound stress responses of other root and tuber crops .....................40 1.6.1. Sweet potato...............................................................................40 v 1.6.2. Yam ............................................................................................41 1.6.3. Taro (Aroids)...............................................................................41 1.6.4. Potato .........................................................................................42 1.7. Genetic transformation in cassava ....................................................43 Chapter 2. Materials and Methods ...........................................................45 2.1. Plant materials ..................................................................................46 2.1.1. Cassava .....................................................................................46 2.1.2. Friable Embryogenic Callus (FEC) of cassava ............................46 2.1.3. Cassava in vitro culture ..............................................................46 2.1.4. Arabidopsis .................................................................................46 2.2. Antibiotics for bacterial and transgenic line selection
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