Plant communities; Agriculture; Genetics; Plants; Fungi; Epigenetics; 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
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.
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.
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.
Rosikiewicz Pawel, Bonvin Jérémy, Sanders Ian R. (2017), Cost-efficient production of in vitro Rhizophagus irregularis, in Mycorrhiza
, 27(5), 477-486.
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.
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.