Insights into the adaptation of Cenococcum geophilum to serpentine soil: ecology and genomics combined (CENECOGEN)
Coordinator - Ludo Muller
Programme - PTDC/BIA-BEC/100733/2008
Execution dates - 2010-01-01 - 2013-06-30 (42 Months)
Funding Entity - Fundação para a Ciência e Tecnologia
Total Funding - 200 000 €
Proponent Institution -
Participating Institutions
Faculdade de Ciências e Tecnologia da Universidade de Coimbra (FCTUC), Portugal
Freie Universität Berlin, Germany

As sessile and long-lived organisms, trees have a limited adaptive potential and are thought to respond to abiotic stress by means of a large phenotypic plasticity and through association with ectomycorrhizal fungi. In the symbiotic association between a tree and an ectomycorrhizal fungus, the tree relies on the fungus to fulfill its nutrient requirements and, in exchange, the fungus receives carbohydrates produced in photosynthesis. Given their central role in carbon and nutrient cycles, ectomycorrhizal fungi are regarded as strong drivers of ecosystem processes.
Ectomycorrhizal fungi are believed to assist trees in colonizing serpentine soils. These globally distributed soils are derived from ultramafic bedrock and often present a major challenge to exposed plants and fungi due to their extreme edaphic conditions: elevated concentrations of heavy metals, low concentrations of essential nutrients, a low calcium-to-magnesium ratio and a low water retention capacity. Despite these disfavourable conditions, adaptive serpentine tolerance is both geographically and phylogenetically widespread, which renders these soils into systems particularly suited for studying the process of adaptive evolution in nature.
Cenococcum geophilum Fr. is a cosmopolitan ectomycorrhizal fungus that can be found in serpentine soil, and recent studies suggested that constitutive drought tolerance and adaptively evolved tolerance to nickel contribute to its serpentine tolerance (Gonçalves et al. 2007, 2009). However, the exact mechanisms and genetic components of this tolerance trait remain unknown and therefore we propose a genome-wide study to identify genetic loci associated with serpentine tolerance in C. geophilum.
We are particularly interested in the contribution of heavy metal tolerance to the multifactorial trait of serpentine tolerance in C. geophilum, and therefore intend a genome-wide association mapping to identify loci specifically associated with nickel tolerance.
Because genomic resources are currently unavailable for C. geophilum, the project will involve determination of its genome sequence using recently developed massively parallel sequencing technology. Genome sequence information will be obtained for both a serpentine tolerant and a serpentine sensitive isolate, which will allow the development of an oligonucleotide microarray platform suited for high-throughput and large-scale genotyping of C. geophilum isolates. Association mapping will be performed using phenotype data obtained with an in vitro nickel sensitivity assay and genotype data obtained with the forementioned microarray platform for C. geophilum isolates collected from serpentine and nonserpentine soils. In addition, the collected data will be analyzed using environmental association mapping and genome scanning for selective sweeps in order to identify genetic loci that are associated with traits other than nickel tolerance that contribute to serpentine tolerance.
Expected results of this project will provide insight into the mechanisms underlying adaptive serpentine tolerance in C. geophilum: information will be obtained about the number of loci involved in nickel tolerance and their chromosomal location, and additional traits, other than nickel tolerance, that contribute to serpentine tolerance in C. geophilum may be revealed. In addition,
development of genomic resources for C. geophilum will be a major benefit to the international ectomycorrhizal research community and will provide a good basis for the establishment of C. geophilum as a model species for studies in ecological genomics of ectomycorrhizal fungi.