A Global Genetic Diversity Analysis of Fusarium Oxysporum F.Sp. Cubense the Panama Disease Pathogen of Banana
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the Panama disease pathogen of banana banana of disease pathogen the Panama analysis of genetic diversity A global A global genetic diversity analysis of Fusarium oxysporum f.sp. cubense the Panama disease pathogen of banana Nadia Ordóñez R. Fusarium oxysporum Fusarium f.sp. f.sp. cubense Nadia Ordóñez R. Nadia Ordóñez 2018 Propositions 1. A multiple marker analysis of the pathogen Fusarium oxysporum f.sp. cubense combined with vegetative compatibility characterization is the most efficient strategy for revealing its population structure. (this thesis) 2. The current nomenclature of races in Fusarium oxysporum f.sp. cubense is inadequate and hence obsolete. (this thesis) 3. The possibility of off-target alterations (Baltimore et al., 2015 Science 348, 36-38) should not limit the application of CRISPR genomic engineering technology in plants or even humans. 4. Computer vision recognition built on last century images risks to recreate previous gender biases into robots (Zhao et al., 2017, In Proceedings of the Conference on Empirical Methods in Natural Language Processing, Denmark, 2979-2989). 5. The only justification for an army to exist nowadays is a response to senseless hostility where dialog is not feasible. 6. Science only contributes to human progress if combined with business ideas and humanity. Propositions belonging to the PhD thesis, entitled: A global genetic diversity analysis of Fusarium oxysporum f.sp. cubense, the Panama disease pathogen of banana Nadia Ordóñez R. Wageningen, 16 October 2018 A global genetic diversity analysis of Fusarium oxysporum f.sp. cubense the Panama disease pathogen of banana Nadia Ordóñez R. A global genetic diversity analysis of Fusarium oxysporum f.sp. cubense the Panama disease pathogen of banana Nadia Ordóñez R. Thesis committee Promotor Prof. Dr G.H.J. Kema Special Professor Tropical Phytopathology Wageningen University & Research Co-promotors Dr M.F. Seidl Assistant Professor at the Laboratory of Phytopathology Wageningen University & Research Dr H.J.G. Meijer Post Doc at Wageningen Plant Research Wageningen University & Research Other members Prof. Dr A. di Pietro, University of Córdoba, Spain Prof. Dr A.F.J.M. van den Ackerveken, Utrecht University Thesis Prof. Dr M.E. Schranz, Wageningen University & Research submitted in fulfillment of the requirements for the degree of doctor Dr J.J. Stoorvogel, Wageningen University & Research at Wageningen University by the authority of the Rector Magnificus, Prof. Dr A.P.J. Mol, in the presence of the Thesis Committee appointed by the Academic Board This research was conducted under auspices of the Graduate School Experimental Plant to be defended in public Sciences (EPS). on Tuesday 16 October 2018 at 4 p.m. in the Aula. A global genetic diversity analysis of Fusarium oxysporum f.sp. cubense the Panama disease pathogen of banana Nadia Ordóñez R. Thesis committee Promotor Prof. Dr G.H.J. Kema Special Professor Tropical Phytopathology Wageningen University & Research Co-promotors Dr M.F. Seidl Assistant Professor at the Laboratory of Phytopathology Wageningen University & Research Dr H.J.G. Meijer Post Doc at Wageningen Plant Research Wageningen University & Research Other members Prof. Dr A. di Pietro, University of Córdoba, Spain Prof. Dr A.F.J.M. van den Ackerveken, Utrecht University Thesis Prof. Dr M.E. Schranz, Wageningen University & Research submitted in fulfillment of the requirements for the degree of doctor Dr J.J. Stoorvogel, Wageningen University & Research at Wageningen University by the authority of the Rector Magnificus, Prof. Dr A.P.J. Mol, in the presence of the Thesis Committee appointed by the Academic Board This research was conducted under auspices of the Graduate School Experimental Plant to be defended in public Sciences (EPS). on Tuesday 16 October 2018 at 4 p.m. in the Aula. Nadia Ordóñez R. A global genetic diversity analysis of Fusarium oxysporum f.sp. cubense, the Panama disease pathogen of banana, 1506 pages. PhD thesis, Wageningen University, Wageningen, the Netherlands (2018) With references, with summaries in English, Spanish and Dutch ISBN 978-94-6343-298-6 DOI https://doi.org/10.18174/453455 Contents Chapter 1 General introduction 7 7 Chapter 2 Worse comes to worst: Bananas and Panama disease – when 23 25 plant and pathogen clones meet Chapter 3 A Loop-Mediated Isothermal Amplification assay based on 34 37 unique markers derived from genotyping by sequencing data for rapid in-plant diagnosis of Fusarium oxysporum f.sp. cubense tropical race 4 in banana Chapter 4 The phylogeography of the banana Fusarium wilt pathogen 55 59 Fusarium oxysporum f.sp. cubense Chapter 5 Unveiling the pathogenicity of the widest array of genetically 95101 diverse Fusarium oxysporum f.sp. cubense isolates on ‘Gros Michel’ and ‘Grand Naine’ banana cultivars Chapter 6 General discussion 111213 Summaries 132141 Acknowledgements 147 About the author 151 Nadia Ordóñez R. A global genetic diversity analysis of Fusarium oxysporum f.sp. cubense, the Panama disease List of publications 152 pathogen of banana, Education statement of the Graduate School 154 150 pages. Experimental Plant Sciences PhD thesis, Wageningen University, Wageningen, the Netherlands (2018) With references, with summaries in English, Spanish and Dutch ISBN 978-94-6343-298-6 DOI https://doi.org/10.18174/453455 Chapter 1 Introduction Chapter 1 Introduction C HAPTER 1 “Whatever you do will be insignificant, but it is very important that you do it.” CHAPTER 1 “Whatever you do will be insignificant, but it is very important that you do it.” ― Mahatma Gandhi ― Mahatma Gandhi General introduction General introduction 7 7 Chapter 1 Introduction Chapter 1 Introduction C HAPTER 1 “Whatever you do will be insignificant, but it is very important that you do it.” CHAPTER 1 “Whatever you do will be insignificant, but it is very important that you do it.” ― Mahatma Gandhi ― Mahatma Gandhi General introduction General introduction 7 7 Chapter 1 Introduction BANANAS:ChapterChapter 1 Introduction1 IMPORTANCE, ORIGIN AND FUNGAL DISEASES Chapter 1 Introduction Bananas are an essential staple food for developing countries, particularly in Africa whereBANANAS: the consumption IMPORTANCE, of banana ORIGIN is higher AND than FUNGAL in Asia DISEASES and Latin America, and generates The modern range of commercially cultivated banana varieties (cultivars) originated in substantialBananas economic are incomean essential for smallstaple foodand largefor developing producers cou (Frisonntries, &particularly Sharrock, in 1998)Africa. As the Indo-Malayan archipelago in Southeast Asia (Heslop-Harrison & Schwarzacher, 2007; staplewhere food the with consumption a high carbohydrate of banana is content higher (Parthaneek, in Asia 2016) and, bananas Latin America, are an importantand generates calorie Perrier et al., 2011), where domestication started around 7,000 years ago (D'Hont et al., sourcesubstantial in the dieteconomic of over income 500 million for small inhabitants and large in producers banana producing (Frison & countries Sharrock, (Aurore 1998). Aset al., 2012). The domestication from wild to edible, hence seedless, bananas involved natural 2009)staple. Bananas food with are a nothigh only carbohydrate eaten raw content as dessert (Pareek, or sweet2016), bananas,bananas are but an also important cooked calorie such as hybridizations between diverse species and subspecies, facilitated by human transportation of plantainssource inand the cooking diet of over bananas. 500 million Additionally, inhabitants theyin banana are producingused as rawcountries materials (Aurore in et diverse al., plants, as well as parthenocarpy, a phenomenon where fertile diploid bananas develop 2009). Bananas are not only eaten raw as dessert or sweet bananas, but also cooked such as seedless fruits (D'Hont et al., 2012; Heslop-Harrison & Schwarzacher, 2007; Perrier et al., regional products, for instance in beer, juice or flour production (Aurore et al., 2009; Ekesa et plantains and cooking bananas. Additionally, they are used as raw materials in diverse 2011). From Southeast Asia, bananas were eventually transported to Africa by early human al., 2012). Equally important, bananas are a cash crop for small farmers that serve domestic regional products, for instance in beer, juice or flour production (Aurore et al., 2009; Ekesa et migration, and later to America during the colonization (D'Hont et al., 2012; Marin et al., marketsal., 2012) and .for Equally banana important, producing bananas countries are aexporting cash crop to for international small farmers markets that serve. Nearly domestic 85% of 1998; Perrier et al., 2011; Robinson & Sauco, 2010), where multinational companies the mtotalarkets production and for banana of producingbananas countriesis designated exporting to tolocal international markets markets and .only Nearly 15% 85% entersof contributed to building “banana republic” empires across Central and South America (Jansen, internationalthe total productionmarkets (FAOSTAT, of bananas 2013)is designated. In 201 4,to worldlocal marketsbanana productionand only 15% reached enters 7 8.8 2006; Koeppel, 2008). 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