The life cycles and dispersal of edible fungi are still poorly known, thus limiting our understanding of their evolution and domestication. The prized Tuber melanosporum produces fruitbodies (fleshy organs where meiospores mature) gathered in natural, spontaneously inoculated forests or harvested in plantations of nursery-inoculated trees. Yet, how fruitbodies are formed remains unclear, thus limiting yields, and how current domestication attempts affect population genetic structure is overlooked. Fruitbodies result from mating between two haploid individuals: the maternal parent forms the flesh and the meiospores, while the paternal parent only contributes to the meiospores. We analyzed the genetic diversity of T. melanosporum comparatively in spontaneous forests versus plantations, using SSR polymorphism of 950 samples from South-East France. All populations displayed strong genetic isolation by distance at the metric scale, possibly due to animal dispersal, meiospore persistence in soil, and/or exclusion of unrelated individuals by vegetative incompatibility. High inbreeding was consistently found, suggesting that parents often develop from meiospores produced by the same fruitbody. Unlike maternal genotypes, paternal mycelia contributed to few fruitbodies each, did not persist over years, and were undetectable on tree mycorrhizae. Thus, we postulate that germlings from the soil spore bank act as paternal partners. Paternal genetic diversity and outbreeding were higher in plantations than in spontaneous truffle-grounds, perhaps because truffle growers disperse fruitbodies to maintain inoculation in plantations. However, planted and spontaneous populations were not genetically isolated, so that T. melanosporum illustrates an early step of domestication where genetic structure remains little affected.

Truffle genotyping dataOpen document files (.odt) of genotyping data (11 to 13 microsatellites and mating-type) at three different sampling scales (described in the manuscript). Each file contain a first slide with the description of column names and several slides for the data from the different samplings sites (brûlés or truffle-grounds).Truffle-genotyping_data.zipzygotes genotypes & scriptZygotic genotypes and R script to estimate heterozygote deficits from the zygotic genotype obtained by spore extraction from Tuber melanosporum fruitbodies sampled at brûlé scale (PB1, PB2, PB3, SB1, SB2). For each locus, the first allele corresponds to the maternal one (genotype of the gleba) and the second one to the paternal one (detected after spore extraction).