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The Tolerance of Wheat (Triticum Aestivum L.) to Septoria Tritici Blotch François Collin

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The Tolerance of Wheat (Triticum Aestivum L.) to Septoria Tritici Blotch François Collin The tolerance of wheat (Triticum aestivum L.) to Septoria tritici blotch François Collin To cite this version: François Collin. The tolerance of wheat (Triticum aestivum L.) to Septoria tritici blotch. Agronomy. Institut agronomique, vétérinaire et forestier de France; University of Nottingham, 2017. English. NNT : 2017IAVF0028. tel-02443529 HAL Id: tel-02443529 https://pastel.archives-ouvertes.fr/tel-02443529 Submitted on 17 Jan 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. NNT : 2017 IAVF 0028 THESE DE DOCTORAT préparée à l’Institut des sciences et industries du vivant et de l’environnement (AgroParisTech) pour obtenir le grade de Docteur de l’Institut agronomique, vétérinaire et forestier de France Spécialité : sciences agronomiques École doctorale n°581 Agriculture, alimentation, biologie, environnement et santé (ABIES) par François COLLIN The tolerance of wheat (Triticum aestivum L.) to Septoria tritici blotch La tolérance du blé (Triticum aestivum L.) à la septoriose Directeurs de thèse : Marie-Odile BANCAL, John FOULKES Co-encadrement de la thèse : Pierre BANCAL Thèse présentée et soutenue à Sutton Bonington (Royaume Uni), le 12 décembre 2017 : Composition du jury : Dr. Ian BINGHAM, Reader in Crop Physiology, Scotlands Rural College Président, Examinateur Dr. Matthew DICKINSON, Professor of Plant Pathology, University of Nottingham Rapporteur UMR ÉcoSys (INRA/AgroParisTech) University of Nottingham, Plant and Crop Sciences Route de la ferme Sutton Bonington Campus 78850 Thiverval-Grignon Leicestershire LE12 5RD FRANCE ROYAUME UNI The tolerance of wheat (Triticum aestivum L.) to Septori tritici blotch La tolérance du blé (Triticum aestivum L.) à la septoriose A thesis submitted to: the University of Nottingham, School of Bioscience (Sutton Bonington, United Kingdom) and l’École doctorale Agriculture, Alimentation, Biologie, Environnement et Santé — ABIES, AgroParisTech (Paris, France). Prepared by François Collin for the dual-award of the degree of Doctor of Philosophy and the grade of Docteur de l’Institut agronomique, vétérinaire et forestier de France. October 2017 Acknowledgments This work would not have been possible without the participation of Arvalis, the University of Nottingham and the UMR ECOSYS (AgroParisTech, INRA). I am proud to have been part of these organisations which carry project, support research and provide an environment for scientific achievement. Firstly, I am grateful to Marie-Odile and Pierre Bancal and John Foulkes who super- vised the PhD project. They provided eective guidance and support. They have also taught me complementary methods and approaches which, I hope, spread through this study. Besides, they encouraged my participation in conferences which were good oppor- tunities to communicate about my work and to confront with the scientific community. If I obviously have a profound respect for them as scientists, I also appreciate their sympathy, kindness and encouragement which are an inspiration for me. Thank you very much. My participation in this project would not have been possible if I had not met Jean- Charles Deswarte and David Gouache. They showed a large enthusiasm for my partic- ipation in this project and helped for a smooth and eective transition from my former position to this study. They regularly contributed to the project, bringing ideas and com- plementary standpoint on the project. Beyond the scientific input they provided, they also helped me to take confidence in my work and emphasised the professional relevancy of it. In addition, many people fed the scientific discussion and helped us during the French steering committees, the ADAS meetings of the tolerance project restitution and other meetings. I am therefore grateful to Neil Paveley, Julie Smith, Femke van den Berg, David Causeur, Frank van den Bosch, Pierre Casadebaig, Bénédicte Quilot-Turion, Mickaël Chelle for their respective contributions. Moreover, I want to thank Larissa Ondo, Julie Rodrigues, Maxime Marques, Fabrice Duhamel for their implication in the glasshouse experiment. I am thankful for the assis- tance and the good company of Dennis Churchill and James Durnford during my stay for the field experiment in Hereford. I thank Jayalath De Silva who organised eective technical assistance and training in Sutton Bonington as well as Dongfang Li who has been very kind and helpful for the chemical analysis. Finally, the PhD project was personally demanding because of the alternate periods in i the UK and in France. However, it was also an incredible enrichment. I would never have imagined that I would meet so many people from so many shores in such a short time. They have been supportive, helping colleagues, supporting friends, housemates, tourists (!), I am keen to thank: Marion, Gita, Helena, Maike, Verena, Alfonso, Becca, Kate, Ajit, Shadia, Kamal, Letizia, Iride and Anna. Thank you, merci and dziękuję! ii Abstract The Septoria tritici blotch disease (STB, pathogen Zymoseptoria tritici) is the most damaging foliar infection of wheat crops in Europe. Disease management strategies in- clude cultivar resistance, disease escape strategy and fungicides. However, these strate- gies have failed to provide a complete protection of wheat crops. The STB tolerance is a complementary approach which aims to maintain yield in the presence of the symptoms. The tolerance of STB relies on plant physiology and source/sink balance: the sink demand (the grain growth) must be satisfied in spite of reduced source availability (pho- tosynthetic capacity as aected by the STB symptoms on the leaves). The green canopy area, the senescence timing and the grain yield components are interesting potential sources of tolerance that were studied in this project. A data-mining study, one glasshouse experiment and two field experiments were car- ried out providing complementary insights on STB tolerance mechanisms. The genotype × environment interaction eects on tolerance traits were investigated for two seasons × five locations × nine cultivars datasets. The nitrogen nutrition and metabolism of four doubled-haploid (DH) lines contrasting for STB tolerance were examined in a controlled- glasshouse experiment at UMR ECOSYS (INRA,AgroParisTech) Grignon, France. The source/sink balance of six DH lines contrasting for STB tolerance was also examined ac- cording to their responses to a spikelet removal treatment, applied in a field experiment in Hereford, UK. Finally, a field experiment with two fungicide regimes (full disease con- trol and non-target (STB) disease control) probed the STB tolerance of six modern UK winter wheat cultivars in Leicestershire, UK. The main objective was to verify identified potential STB tolerance traits in commercial cultivars. Putative STB tolerance traits have been identified such as the early heading date, the low degree of grain-source limitation of healthy crops during the grain filling phase, the vertical canopy distribution favouring a relatively larger flag-leaf. Results showed these traits might be selectable in wheat breeding without a trade-o with the potential yield. Finally, the project also discussed the need for alternative STB tolerance quantification methods, as well as the importance of environmental variations which have to be taken into account to study genetic variation in tolerance, but which could also be used to discriminate tolerant environment. iii Contents 1 Introduction and Literature Review1 1.1 Introduction..................................1 1.2 Literature Review...............................2 1.2.1 Potential yield.............................3 1.2.1.1 Overview of the wheat physiology: growth and development4 The wheat development until anthesis............4 The grain filling phase....................6 The source/sink manipulations and grain yield limitation.6 1.2.1.2 Fate of Nitrogen and Carbon fluxes during the senescence7 The end of nitrogen uptake..................8 Senescence and N remobilisation.............. 10 Senescence and reduction of carbon assimilation...... 13 1.2.1.3 An equation for potential yield.............. 15 1.2.2 Stress, strain and tolerance of Septoria tritici blotch........ 17 1.2.2.1 The Septoria tritici blotch: a biotic stress of wheat crops 18 Life cycle of Zymoseptori tritici ................ 19 Plant × pathogen interactions................ 20 1.2.2.2 Methods for crop control of STB............. 21 Breeding for resistance.................... 21 Avoidance and sanitary measures.............. 22 Fungicide-based control.................... 23 1.2.2.3 Quantify the tolerance of Septoria tritici blotch..... 25 1.2.3 Identification of STB tolerance traits................ 25 1.3 Rationale, objectives and hypotheses..................... 29 References...................................... 30 2 Materials and methods 43 2.1 Introduction.................................. 43 Introduction..................................... 43 2.2 Overview of the study methods........................ 44 2.2.1 Data mining.............................. 44 2.2.2 Field experiment 2014-15......................
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