16 17 Running title: Molecular genetic mechanisms of Zn tolerance in Suillus 18 2 Originality -significance statement 19To the best of our knowledge, this is the first study linking genotypes to adaptive phenotypes in 20 mycorrhizal fungi. It is unique in the way it combines evolutionary and functional genetics to allow 21 a significant advance in the understanding of responses to environmental stress factors in general 22 and, to soil metal pollution in particular. A better understanding of adaptive tolerance mechanisms 23 in keystone symbiotic fungi is paramount for developing impactful phyto and mycoremediation 24 strategies for metal polluted waste land and to predict the impact of future environmental change 25 on mycorrhizal diversity and ecosystem functioning. 26 3 Summary 27 Abiotic changes due to anthropogenic activities affect selection regimes for organisms. How trees 28 and their mycorrhizal symbionts adapt to altered environments in heterogeneous landscapes is of 29 great interest. With a global distribution and multiple adaptive phenotypes available, Suillus luteus 30 is an excellent ectomycorrhizal model to study evolutionary dynamics of local adaptation. We 31 assessed pathways of homeostasis and detoxification in S. luteus isolates, displaying contrasting 32 Zn tolerance phenotypes to identify mechanisms underlying adaptive Zn tolerance. Using 30 33 randomly selected isolates sampled at metal contaminated and control sites, we documented Zn 34 tolerance phenotypes, assessed the link with identified candidate genes and explored its genetic 35 basis via targeted amplicon sequencing and qPCR. Zn tolerance phenotypes covering a continuum 36 from Zn sensitive to hypertolerant were identified and inversely correlate with cellular Zn 37 accumulation. Gene expression of SlZnT2, encoding a putative Zn transporter explains 72% of the 38 observed phenotypic variation. SlZnT2 copy number varies among isolates and different promotor 39 genotypes were identified. Rapid adaptation in this species is supported by the cumulative effect of 40 gene copy number variation and differences in cis-regulation and might be triggered by 41 environmental stress rather than being the result of standing variation. 42 43 Keywords 44 Cation Diffusion Facilitator, Copy Number Variation, environmental adaptation, gene expression, 45 mycorrhiza, Suillus, zinc 46 69 al., 2004; Colpaert et al., 2011). Adaptive phenotypes of these species presumably support the 70 establishment of pines on severely contaminated soils (Colpaert et al., 2011). Evolutionary 71 dynamics of local adaptation and the genomic features governing the adaptive potential of these 72 particular Suilloid species are as for other ectomycorrhizal fungi not yet explored despite their 73 putative importance for the understanding of pine establishment on waste lands.74 Rapid adaptation to strong human induced shifts in the environment is repeatedly linked to discrete 75 traits. Discrete traits are traits with only a few possible phenotypes, clearly falling in discrete ...