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Cereal Cyst Nematodes: Molecular Ldentification and Quantification, and Screening for Resistance in Wheat

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+ ~ t ~ I !-+-+++~ I I I I I Cereal Cyst Nematodes: Molecular ldentification and Quantification, and Screening for Resistance in Wheat Fateh TOUMI ............ 1111111 GHENT ft;.~, FACULTY OF UNIVERSITY ~ BIOSCIENCE ENGINEERING I Promoters: Prof. Em. dr. ir. Maurice Moens Department of Crop Protection Faculty of Bioscience Engineering Ghent University, Belgium Prof. dr. ir. Nicole Viaene Department of Biology Faculty of Science Ghent University, Institute for Agricultural and Fisheries Research (ILVO), Merelbeke, Belgium Prof. dr. ir. Luc Tirry Department of Crop Protection Faculty of Bioscience Engineering Ghent University, Belgium Dean: Prof. Dr. ir. Marc Van Meirvenne Rector: Prof. Dr. Anne De Paepe II Fateh TOUMI Cereal cyst nematodes: molecular identification and quantification, and screening for resistance in wheat Thesis submitted in fulfillment of the requirements for the degree of Doctor (PhD) in Applied Biological Sciences III Dutch translation of the title: Graancystenematoden: moleculaire identificatie en kwantificatie, en screening voor resistentie in tarwe. Illustration on the front cover: from up left to right, enlarged white females of Heterodera latipons attached to roots; field screening for resistance to H. avenae, symptoms of H. filipjevi damage in the field, and second-stage juvenile of H. filipjevi. Illustration on the back cover: qPCR from dilution series of DNA extracted from 120 J2 to quantify H. avenae. Citation: Toumi, F. (2017). Cereal Cyst Nematodes: molecular identification and quantification, and screening for resistance in wheat. PhD thesis, Ghent University, Ghent, Belgium, 228 p. ISBN 978-90-5989-963-6 The author and promoters give the authorisation to consult and to copy parts of this work for personal use only. Every other use is subject to the copyright laws. Permission to reproduce any material contained in this work should be obtained from the author. The promoters: Prof. dr. ir. Maurice Moens Prof. dr. ir. Nicole Viaene Prof. dr. ir. Luc Tirry The author: ir. Fateh Toumi IV V Sonia, I am Very weak to write about your strength!!! Very strong to be a friend of you!!! Very calm to write about your patience!!! Very jealous of your success!!! Very classic to write about your beauty!!! You are the light of our life, my guide, my love. I am coming back very soon. Soso, I love you!!! VI ACKNOWLEDGEMENTS Foremost, I would like to express my sincere gratitude to my promoter Prof. Maurice Moens, for the constant support of my Ph.D. study and research, for his motivation, and for sharing with me his immense wealth of knowledge. I had the unique privilege of being his master and Ph.D. student. The knowledge acquired is highly appreciated and valued, and now constitutes a strong foundation for my future achievements and success. Also, I would like to thank his wife Mrs. Monique for her kindness. I am profoundly grateful to my co-promoter Prof. Nicole Viaene for her supervision (including strong support for my scientific writing skills), her kindness, great ideas, and patience. I thank her for all the valuable time and effort she generously offered to me. Warm regards for all your family members Patrick, Nuria, and Robin. I also wish to thank Prof. Luc Tirry for his help, encouragement and support during my Ph.D. research and administration issues. Thanks so much for your smiley disposition which, combined with your care and concern, was always very reassuring! My profound gratitude goes to Dr Julie Nicol who guided me during both the MSc and Ph.D. scholarships and has been a role model throughout my research career. She provided direction and valuable advice, which helped to open the door to new ideas and opportunities. I will remain an admirer of her skills, experience and personal dedication to the professional development of young talent. I would like to express my special appreciation to Dr Francis Ogbonnaya for his strong support and understanding, for the time we spent preparing the Ph.D. proposal, and for his quick, critical but very constructive comments on all my publications. It was indeed a great joy and honour to work under his supervision. I benefitted immensely from the scientific and emotional support as well as the wonderful moments spent together with Lieven Waeyenberge. He was my MSc advisor, my Ph.D. advisor, a friend, and a brother. He was and still is that person I would consult and discuss the search for solutions to difficult issues, ending with a big smile and strong publications. My sincere gratitude also goes to his wife Nancy, my MSc support, for her patience behind VII the microscope as well as her understanding. Warm regards for your families and a big hug for your lovely son Lennerd. I will not forget you and I will keep contacting you forever. My profound gratitude goes to Dr Abdelfattah Amer Dababat (Habibi) for hosting and supervising me while I conducted field trials in Turkey. His support, constant encouragement, and valuable advice are very highly appreciated. I am also grateful to the Turkish Ministry of Agriculture, especially the Transitional Zone Agriculture Research Institute in Eskisehir and Adana for the technical and logistic support during my stay. I am sincerely grateful to Dr Jan De Riek and his wife Dr Ellen De Keyser for the great support and conducive environment they provided in their lab, which enabled me to carry out high-quality work with very satisfactory results. Dear Ellen and Jan, thanks for the powerful support and the nice time I had in your lab. Sure, I will not forget to thank Mrs. Veerle Buysens and Mrs. Laurence De Smet for their kind and excellent technical assistance in the lab. It was a very nice experience to learn novel techniques, exchange scientific information and discuss some of our traditions and cultures. I also wish to thank Dr Alexey Morgunov for providing the valuable and unique wheat seeds, which allowed me to finish my research, and for his help and advice during the practical work and writing session. His efforts and support are appreciated. Special appreciation is also due to Prof. Wilfrida Decraemer, Nic Smol, Inge Dehennin of the European Master of Science in Nematology (EUMAINE) programme who facilitated and supported the start of my journey into the nematology family in Belgium. I also appreciate all my EUMAINE professors at Ghent University with whom I experienced a remarkable period of my life. The solidarity of my colleagues in both EUMAINE and PINC programmes is gratefully acknowledged. I would also like to take this opportunity to thank my supervisor, Prof. Bassam Bayaa who introduced me to the International Centre for Agricultural Research in the Dry Areas (ICARDA) in Syria to do my first MSc in nematology; and later, Dr. Mathew Abang who inspired me to continue my studies abroad. Prof. Fateh Khatib and Dr. Samer Lababidi† VIII equally provided a lot of encouragement and support. It was a difficult decision to leave my family and to start a new life in Belgium but they helped me make up my mind, take the decision and strive towards my goal of excellence in international agriculture. Many thanks to my wonderful friends, Yao, Branimir and his family (the great wife Aleksandra, Aleksa and Ana), Nikola and his great girlfriend Duska, and Natalia and her son Kyrill. I started life in Belgium with them sharing our thoughts, tough time, ideas and a lot of wonderful moments together. Special appreciation and thanks go to my friend Negin Ebrahimi for always being there for me, giving scientific advice and encouraging me during the tough moments of my Ph.D. It was indeed a great pleasure to share the difficult and good times. I will keep you all in my mind and I will wait for the time you will visit me in Syria. Will miss you all so much!!! Also, I would like to thank all scientists I met during my stay in ICARDA, Dr. Nicola Greco, Dr. Mauro Di Vito, Dr. Amor Yahyaoui, Prof. Wafaa Choumane, Prof. Ahmed El-Ahmed†, Dr. Michael Baum, Dr. Saaed Kemal, Mrs. Siham Kabbabeh, Ms. Sawsan Tawakz, Dr. Aladdin Hamwieh, Prof. Hisham Al-Zainab, and Mr. Samir Hajjar, for their encouragement and support, which helped to put me on the right career path. Also, I was blessed to have some great and very helpful friends based at ICARDA: Basma, Rita, Mouna, Omar, Maha, Lama, Iman, Najah, Nahed, Michael, Kenana, Ali, Nabil, Khaled, Elias, Mohammad, Nouran, Adonis, Fida, Shoual, Ola, Roula, Hani, Hala, Nader. Memories of the many activities we undertook together and the wonderful moments of success and happiness we shared will remain indelible. I acknowledge with thanks the help and kindness received from Dr. Roger Rivoal, Prof. Dr. Richard Smiley, Prof. Dr. Ian Riley, Dr. Mohammad Hamshou, Mr. Rachid Tahzima, Dr. Fouad Mokrini, Dr. Mohammad Amjd Ali, Dr. Omar Idrissi, Dr. Gül Erginbas, Prof. Mustafa Imren, Prof. Halil Elekçioğlu, Prof. Halil Toktay, Prof. Ahmed Al-Hazmi, Prof. Ahmed Dawabah, Prof. Luma Al-Banna, Dr. Zahra Maafi, Dr. Adel Al-Abed, all members of the ICNI family. I would like to thank you for all the support and concern. It was always a pleasure to discuss and consult with them on many issues. IX I would like to thank my dear Syrian friends and colleagues and their families, Nazeh Maoud, Rimoun Makdesie, Dr. Abdalah Khorie, Dr. Bassel Dakhil, Dr. Modar Hadad, Dr. Amer Kazaal, Dr. Abd Al-Masieh Daiej, Dr. Tarad Jwaid, Dr. Karim Haj Ismail, Dr. Hussain Saleh, Mohammad Al-Abed, Mahmoud Hazaa, Mecheal Kasis, Dima, Nsrien, Ola, Shadie, Loura, Bdoor, Kalaaji family, Atiah family, Hadad family, Al-Awil family, Merit family, Makdesie family, Dakhil family, Toumi family, Ibrahim family, Shieha family, Al- Azon family, Nassar family for their support and help during my work and stay in Syria and Belgium.
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  • Molecular Characterization of Cyst Nematode Species (Heterodera Spp.) from the Mediterranean Basin Using Rflps and Sequences of ITS-Rdna

    Molecular Characterization of Cyst Nematode Species (Heterodera Spp.) from the Mediterranean Basin Using Rflps and Sequences of ITS-Rdna

    J. Phytopathology 152, 229–234 (2004) Ó 2004 Blackwell Verlag, Berlin ISSN 0931-1785 Crop Protection Department, Agricultural Research Centre, Merelbeke, Belgium Molecular Characterization of Cyst Nematode Species (Heterodera spp.) from the Mediterranean Basin using RFLPs and Sequences of ITS-rDNA M.Madani 1, N.Vovlas 2, P.Castillo 3, S. A.Subbotin 4 and M.Moens 1,51,5 AuthorsÕ addresses: 1Crop Protection Department, Agricultural Research Centre, Burg, Van Gansberghelaan 96, 9820 Merelbeke, Belgium; 2Istituto per la Protezione delle Piante, Sezione di Bari: Nematologia Agraria, Consiglio Nazionale delle Ricerche (C.N.R.), Via G. Amendola 165/A, 70126 Bari, Italy; 3Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Cientificas (C.S.I.C.), Apdo. 4084, 14080 Cordoba, Spain; 4Institute of Parasitology of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow 119071, Russia; 5University of Gent, Laboratory for Agrozoology, Coupure 555, 9000 Gent, Belgium (correspondence to S. A. Subbotin. E-mail: [email protected]) With 2 figures Received August 6, 2003; accepted February 11, 2004 Keywords: Heterodera carotae, Heterodera ciceri, Heterodera fici, Heterodera filipjevi, Heterodera goettingiana, Heterodera hordecalis, Heterodera humuli, Heterodera mediterranea, Heterodera ripae, Heterodera schachtii, internal transcribed spacer region, phylogenetic relationships, molecular identification Abstract plant growth and yield may be suppressed (Baldwin Fifteen populations of cyst-forming nematodes belong- and Mundo Ocampo, 1991). ing to 11 known and one unidentified species collected Currently, the genus Heterodera contains more than in countries bordering the Mediterranean Sea were 60 species (Wouts and Baldwin, 1998). In the Mediterra- studied using polymerase chain reaction restriction nean Basin several cyst nematode species have been fragment length polymorphism (PCR–RFLP) and reported on herbaceous and woody plants (Greco and internal transcribed spacer (ITS)-rDNA sequences.