A Tool for Design Decision Making

Sommaire

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
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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
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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
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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 Scientific Achievements ............................................ 231
General discussion ................................................................................ 215
Conclusion et perspectives ................................................................... 225
Overview of the Scientific Achievements ............................................ 231
Supplementary data .............................................................................. 231
References .............................................................................................. 251
Annex ................................................................................................. 295