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Does the Arbuscular Mycorrhizal Fungus Rhizophagus Irregularis Mitigate Late Blight in Potato Plants?

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Does the Arbuscular Mycorrhizal Fungus Rhizophagus Irregularis Mitigate Late Blight in Potato Plants? Université catholique de Louvain Faculté des bioingénieurs Earth and Life Institute Pole of Applied Microbiology Laboratory of Mycology Does the arbuscular mycorrhizal fungus Rhizophagus irregularis mitigate late blight in potato plants? Thèse de doctorat présentée par Pierre-Louis ALAUX en vue de l'obtention du grade de Docteur en Sciences agronomiques et ingénierie biologique Promoteur : Prof. S. Declerck (UCLouvain, Belgique) Président du jury : Prof. C. Bragard (UCLouvain, Belgique) Membres du Jury : Prof. A. Legrève (UCLouvain, Belgique) Prof. D. Wipf (uB, France) Dr. J-L. Rolot (CRA-W, Belgique) Dr. H. Dupré de Boulois (DCM, Belgique) Louvain-la-Neuve, February 2020 TABLE OF CONTENT Acknowledgement ......................................................................... 7 List of abbreviation ....................................................................... 9 Glossary ....................................................................................... 13 Summary...................................................................................... 15 Outline of the thesis .................................................................... 17 Author’s contribution ................................................................. 21 Introduction ............................................................................................. 23 State of the art ......................................................................................... 27 I. Arbuscular mycorrhizal fungi ........................................................ 27 1. Introduction ............................................................................... 27 2. The AMF life cycle ................................................................... 29 a. Pre-symbiotic communication: the role of root and fungal exudates .................................................................................... 31 b. Plant contact and colonization .......................................... 32 c. Arbuscules formation ........................................................ 33 d. Late stage of AMF ............................................................ 35 3. Plant-AMF exchanges and symbiosis control ........................... 35 4. Taxonomy, phylogeny and traceability of AMF ....................... 36 a. First step of classification ................................................. 36 b. Molecular classification .................................................... 37 c. International culture collection ......................................... 38 d. Markers for phylogenetic analyses ................................... 39 e. Traceability of AMF ......................................................... 40 II. Benefits and agronomic applications of AMF ............................. 41 1. Introduction ............................................................................... 41 2. Ecosystem services provided by AMF to agriculture ............... 41 a. Impact on plant nutrition ................................................... 41 b. Impact on soil formation and water retention ................... 43 c. Bioregulation of plant development and modification in plant compounds ....................................................................... 44 d. Abiotic stress alleviation by AMF .................................... 45 e. Biotic stress mitigation by AMF ....................................... 46 3 3. Impact of agronomic practice on AMF ..................................... 69 4. AMF diversity in arable soil ..................................................... 71 5. AMF functional diversity and plant breeding program ............ 72 III. Pathosystem .................................................................................. 72 1. Solanum tuberosum ................................................................... 72 a. History of potato domestication ........................................ 72 b. Potatoes genetic characteristics ......................................... 73 c. Potato production .............................................................. 73 d. Market price and pest management cost ........................... 74 e. Nutritional value of potatoes ............................................. 74 2. Phytophtora infestans ............................................................... 75 a. Introduction ....................................................................... 75 b. Life cycle of Phytophthora infestans ................................ 76 c. Sexual reproduction .......................................................... 77 d. Infection models ............................................................... 77 e. Phytophthora infestans molecular marker ........................ 78 f. Potato defense response against P. infestans .................... 78 3. Late blight management ............................................................ 79 a. Introduction ....................................................................... 79 b. Late blight management via copper .................................. 80 c. Integrated late blight management .................................... 80 d. Beneficial microorganism and late blight management .... 81 e. Regulation framework ...................................................... 91 IV. Plant defense ................................................................................. 92 1. Introduction ............................................................................... 92 a. Pathogen recognition ........................................................ 93 b. The “Zig Zag” model ........................................................ 93 c. Plant defense: hormones and genes .................................. 95 d. Systemic plant defense induction ...................................... 95 2. Pathogen-induced systemic acquired resistance (SAR) ............ 96 3. Induced systemic resistance (ISR) by beneficial microbes ....... 97 4. Priming ...................................................................................... 98 4 a. Introduction ....................................................................... 98 b. Priming defense triggers ................................................... 99 c. Priming steps ..................................................................... 99 d. Epigenetic part of priming .............................................. 100 e. Primed state ..................................................................... 100 5. Mycorrhiza induced resistance ............................................... 101 a. Introduction ..................................................................... 101 b. Mycorrhiza induced resistance in belowground plant parts 102 c. Mycorrhiza induced resistance and systemic response ... 104 6. Common mycorrhizal network ............................................... 105 a. Introduction ..................................................................... 105 b. Nutrients carrier .............................................................. 105 c. Defense signal carrier ..................................................... 106 Research objectives ............................................................................... 109 Material and Methods .......................................................................... 111 I. Organisms ...................................................................................... 111 II. Study model and experimental set up ........................................ 112 1. Mycelium donor plant (MDP) in vitro culture system ............ 113 2. Greenhouse and Field experiment........................................... 114 a. Pre-mycorrhization of potato sprouted tuber .................. 114 b. Field trials setups ............................................................ 116 III. Organisms assessment ............................................................... 119 1. Density of AMF propagules evaluated by the Most Probable Number (MPN) method ................................................................. 119 2. Root colonization of AMF evaluated by Mc Gonigle et al. (1990) method. ............................................................................... 122 3. Late blight inoculation and evaluation of infection under controlled conditions ...................................................................... 124 IV. Molecular methods ..................................................................... 125 1. Selection of genes for RT-qPCR analyses .............................. 125 a. Reference genes .............................................................. 125 b. Target genes .................................................................... 126 5 2. Relative quantification in RT-qPCR ....................................... 128 Research results .................................................................................... 131 Chapter I. Tracing native and inoculated Rhizophagus irregularis in three potato cultivars (Charlotte, Nicola and Bintje) grown under field conditions .................................................................................. 133 Chapter II. Impact of Rhizophagus irregularis MUCL 41833 on disease symptoms caused by Phytophthora infestans in potato grown under field conditions ....................................................................... 159 Chapter III. Interplant signaling via common mycorrhizal networks might warn uninfected potato plants from late blight outbreak .. 189 Overview of the
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