Data from: How the truffle got its mate: insights from genetic structure in spontaneous and planted Mediterranean populations of Tuber melanosporum

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.

目前学界对食用菌的生活史与扩散机制仍缺乏深入认知，这制约了我们对其演化与驯化过程的理解。备受推崇的黑孢块菌（Tuber melanosporum）可产生子实体——即孢子成熟的肉质器官，其子实体可在自然自发接种的森林中被采集，或在苗圃预先接种树木的人工林内收获。然而，子实体的形成机制仍未阐明，这制约了产量提升；同时当前驯化实践如何影响种群遗传结构的相关研究也被忽视。子实体由两个单倍体个体交配产生：母本负责形成肉质结构与孢子，父本仅参与孢子的形成。本研究利用采自法国东南部的950份样本的简单序列重复（Simple Sequence Repeat, SSR）多态性标记，对自发林与人工林内的黑孢块菌遗传多样性进行了比较分析。所有种群在空间尺度上均表现出显著的距离隔离效应，这可能与动物介导的孢子扩散、孢子在土壤中的留存，以及营养体不亲和性对非亲缘个体的排斥作用有关。本研究始终检测到高水平的近交现象，这表明亲本往往源自同一个子实体产生的孢子。与母本基因型不同，父本菌丝体每个个体仅能参与形成少量子实体，且无法多年留存，同时在树木菌根上也无法被检测到。据此我们推测，土壤孢子库中的萌发体可作为父本参与交配。人工林内的父本遗传多样性与异交率均高于天然块菌林地，这可能是因为块菌种植者通过散播子实体来维持人工林的接种效果。但人工种群与天然种群之间并未出现遗传隔离，这表明黑孢块菌正处于驯化的早期阶段，其种群遗传结构尚未受到显著影响。