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From population genomics to variation in symbiotic effects of mycorrhizal fungi on plants

Titel Englisch From population genomics to variation in symbiotic effects of mycorrhizal fungi on plants
Gesuchsteller/in Sanders Ian
Nummer 162549
Förderungsinstrument Projektförderung (Abt. I-III)
Forschungseinrichtung Département d'Ecologie et d'Evolution Faculté de Biologie et de Médecine Université de Lausanne
Hochschule Universität Lausanne - LA
Hauptdisziplin Botanik
Beginn/Ende 01.12.2015 - 30.11.2018
Bewilligter Betrag 818'406.00
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Alle Disziplinen (2)

Disziplin
Botanik
Oekologie

Keywords (7)

Plant communities; Agriculture; Genetics; Plants; Fungi; Epigenetics; Symbiosis

Lay Summary (Französisch)

Lead
Les champignons mycorhiziens forment des symbioses avec les plantes, les aidant à croître et à acquérir des nutriments essentiels tel que le phosphore. Les différences génétiques entre les champignons mycorhiziens ont un impact sur la réponse de croissance des plantes. Le but du projet est de déterminer quelles parties du génome de ces champignons sont responsables de leurs effets bénéfiques sur les plantes. Le manioc est la plante d’étude du projet, car cette plante est un aliment de base dans de nombreuses régions de la planète, et car elle répond fortement à différentes variétés génétiques de champignons mycorhiziens.
Lay summary

La symbiose mycorhizienne s’établissant entre les champignons mycorhiziens à arbuscules (CMA) et les plantes est probablement la symbiose la plus répandue dans la nature. Plus de 60% de toutes les espèces de plantes vasculaires, incluant toutes les plantes agricoles d’importance mondiale, forment cette symbiose. Depuis des décennies, les évidences des multiples bénéfices que les CMA offrent aux plantes s’accumulent, démontrant l’importance de cette symbiose pour l’écologie et l’agriculture. Deux types de variations génétiques existent chez les CMA. Premièrement, la variation intra-spécifique : différents isolats de l’espèce modèle de CMA, Rhizophagus irregularis, diffèrent génétiquement. Deuxièmement, la variation intra-isolat : cette variation génétique existe à l’intérieur de ces champignons. En effet, la variation intra-isolat dans les régions codantes peut être élevée, et cette variation pourrait être distribuée sur différents noyaux. L’un des buts de ce projet est de séquencer les génomes de noyaux individuels de différents isolats, afin de déterminer si la variation génétique intra-isolat se trouve sur différents noyaux. Un autre but de ce projet est d’établir une association entre la variation génétique chez R. irregularis et les traits quantitatifs des plantes hôtes. Nous proposons des approches innovantes pour établir le lien entre génétique du champignon et phénotype de la plante. Nous allons développer des méthodes bioinformatiques quantitatives innovantes pour étudier l’association génome-phénotype, incorporant des études de transcriptome et de génomique des populations de R. irregularis sur le terrain. Ce projet offre une vue unique sur le rôle de la variation génétique chez les CMA sur cette symbiose si importante et courante.

 

Direktlink auf Lay Summary Letzte Aktualisierung: 25.11.2015

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Publikationen

Publikation
Dual RNA-seq reveals large-scale non-conserved genotype × genotype-specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis
Mateus Ivan D., Masclaux Frédéric G., Aletti Consolée, Rojas Edward C., Savary Romain, Dupuis Cindy, Sanders Ian R. (2019), Dual RNA-seq reveals large-scale non-conserved genotype × genotype-specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis, in The ISME Journal, 1-10.
Within-species phylogenetic relatedness of a common mycorrhizal fungus affects evenness in plant communities through effects on dominant species
Savary Romain, Villard Lucas, Sanders Ian R. (2018), Within-species phylogenetic relatedness of a common mycorrhizal fungus affects evenness in plant communities through effects on dominant species, in PLOS ONE, 13(11), e0198537-e0198537.
Variation in allele frequencies at the bg112 locus reveals unequal inheritance of nuclei in a dikaryotic isolate of the fungus Rhizophagus irregularis
Masclaux Frédéric G., Wyss Tania, Mateus-Gonzalez Ivan D., Aletti Consolée, Sanders Ian R. (2018), Variation in allele frequencies at the bg112 locus reveals unequal inheritance of nuclei in a dikaryotic isolate of the fungus Rhizophagus irregularis, in Mycorrhiza, 28(4), 369-377.
A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis
Savary Romain, Masclaux Frédéric G, Wyss Tania, Droh Germain, Cruz Corella Joaquim, Machado Ana Paula, Morton Joseph B, Sanders Ian R (2017), A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis, in The ISME Journal, 12(1), 17-30.
Cost-efficient production of in vitro Rhizophagus irregularis
Rosikiewicz Pawel, Bonvin Jérémy, Sanders Ian R. (2017), Cost-efficient production of in vitro Rhizophagus irregularis, in Mycorrhiza, 27(5), 477-486.
Population genomics reveals that within-fungus polymorphism is common and maintained in populations of the mycorrhizal fungus Rhizophagus irregularis
Wyss Tania, Masclaux Frédéric G, Rosikiewicz Pawel, Pagni Marco, Sanders Ian R (2016), Population genomics reveals that within-fungus polymorphism is common and maintained in populations of the mycorrhizal fungus Rhizophagus irregularis, in The ISME Journal, 10(10), 2514-2526.

Zusammenarbeit

Gruppe / Person Land
Formen der Zusammenarbeit
Prof. Alia Rodriguez, National University of Colombia, Bogota Kolumbien (Südamerika)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Forschungsinfrastrukturen
- Austausch von Mitarbeitern
Ioannis Xenarios, Swiss Institute of Bioinformatics & Vital-IT Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
Dr. Francis Martin, INRA, Nancy Frankreich (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
Symbiom Tschechische Republik (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Forschungsinfrastrukturen
- Industrie/Wirtschaft/weitere anwendungs-orientierte Zusammenarbeit

Wissenschaftliche Veranstaltungen

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
Microbiome Vortrag im Rahmen einer Tagung Effects of inoculating cassava with genetically similar mycorrhizal fungi on local mycorrhizal fungal communities and why it’s important 10.09.2018 Villars, Schweiz Sanders Ian;
ICOM 9 Vortrag im Rahmen einer Tagung Bringing different disciplines together to answer the “BIG questions” in mycorrhizal research 30.07.2017 Prague, Tschechische Republik Sanders Ian;
ICOM 9 Vortrag im Rahmen einer Tagung Demonstrating the link between genomic variation in R. irregularis and significant differences in plant growth 30.07.2017 Prague, Tschechische Republik Sanders Ian;
Swiss Society for Microbiology Vortrag im Rahmen einer Tagung IMPROVING THE WORLDS FOOD SUPPLY USING MICROBES: THE POWER OF FUNGAL GENETICS 13.06.2016 Bern, Schweiz Sanders Ian;


Verbundene Projekte

Nummer Titel Start Förderungsinstrument
144079 Evolutionary genomics of the mycorrhizal symbiosis 01.10.2012 Projektförderung (Abt. I-III)
182826 From population genomics to variation in symbiotic effects on plants 01.12.2018 Projektförderung (Abt. I-III)
131311 Cassava for food security and sustainability in Colombia: Biotechnological application of mycorrhizal fungi 01.08.2011 Resource not found: 'bd31932a-e257-46d9-9dba-079f6f2c77c6'
159665 A microbial revolution: Improving mycorrhizal fungi to increase cassava productivity in Africa 01.04.2016 Interdisziplinäre Projekte

Abstract

Mycorrhizal symbioses formed between arbuscular mycorrhizal fungi (AMF) and plants are probably the most common symbioses in nature. More than 60% of the world's vascular plant species participate in this symbiosis, including all of the globally important food plants. Over the last few decades, the fungi have repeatedly been shown to confer a number of benefits to plants suggesting that the symbiosis is of high ecological and agricultural importance.Two types of genetic variation exist in AMF. Intra-specific genetic variation exists among isolates of the model AMF sepcies R. irregularis. But another type of genetic variation exists within the fungus itself that is predicted to be spatially separated among nuclei within this coenocytic fungus. However, a paradox exists concerning this type of genetic variability. The reference AMF genome of R. irregularis (isolate DAOM 197198) contains little within-fungus polymorphism and this is confirmed as well by our own sequencing of this fungus. However, biological evidence from experiments with other R. irregularis isolates, as well as ultra-deep sequencing of parts of their genome, reveals a different picture with considerable within-fungus polymorphism in coding regions that seem likely to be located on different nuclei. One focus of this project is to sequence the genomes of individual nuclei from these fungi in order to find out if such variation is located on different nuclei. Secondly, because we have discovered a way to cross the fungi, giving rise to R. irregularis lines that contain alleles from two parents, we will use the same technique to discover whether such crossing represents a simple mixing of genetically different nuclei in a common cytoplasm or whether DNA from nuclei of one parent become incorporated in the nuclei of the other parent. This investigation forms the first objective of this project.Within-fungus and among-fungus genetic variation in R. irregularis both strongly influence plant growth. Genetically novel R. irregularis lines, produced by crossing the fungi also give rise to stong differences in plant growth. In these cases, the effects were observed on the biomass of two of the most globally important crops; rice and cassava. In the case of cassava, the effects were even seen under normal field conditions meaning that there is a huge potential to use AMF genetics to produce more food. However, in order to do that, the link needs to be made between genetic variation in the fungus and quantitative growth traits in the plant. This is made more complicated by the fact that: 1. Genetic variability in R. irregularis lines can be qualitative (e.g. presence and absence of a SNP at a given locus) or quantitative (changes in allele frequency at given loci). 2. The fungal genotype can be rapidly altered by a shift of host plant. 3. In natural and agricultural conditions, inoculated plants also become colonized by local AMF. The second goal of this project is, therefore, to establish if detectable associations can be found between genetic variation in R. irregularis and quantitative traits of plant growth. Given the three unusual complications above, we propose highly novel ways to try and establish this link between fungal genotype and plant phenotype. This involves the development of completely novel quantitative bioinformatics tools for genome-wide association studies that also incorporate in-field transcriptome expression of the fungus and population genomics of R. irregularis in the field. This project can provide a unique insight into the role of genetic variation of AMF in this important and very common symbiosis.
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