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.

食用菌的生活史与扩散机制迄今仍鲜有研究，这极大限制了学界对其演化与驯化进程的认知。备受青睐的黑孢块菌（Tuber melanosporum）所产生的子实体（fruitbodies）——即承载减数孢子成熟的肉质组织结构——既可在自然自发接种的森林中采集，也可在苗圃培育接种树木的人工林内收获。然而，子实体的形成机制至今仍不明晰，这不仅制约了块菌产量的提升，同时当前驯化实践对其种群遗传结构的影响也尚未得到系统关注。子实体的形成源于两个单倍体个体的交配：母本亲本可形成肉质组织与减数孢子，而父本亲本仅贡献减数孢子。本研究针对法国东南部的950份样本开展简单序列重复（Simple Sequence Repeats，SSR）多态性分析，对比了自然自发林与人工林中黑孢块菌的遗传多样性。所有种群在空间尺度上均表现出显著的距离隔离效应，这一现象可能由以下因素导致：动物介导的孢子扩散、土壤中减数孢子的长期留存，以及/或营养体不亲和性对非亲缘个体的排斥作用。研究始终检测到高水平的近交现象，这表明亲本通常源自同一子实体产生的减数孢子。与母本基因型不同，父本菌丝体仅参与形成少量子实体，且无法多年持续存在，同时在树木菌根（mycorrhizae）上无法被检测到。据此我们推测，土壤孢子库中的萌发体可作为父本交配配偶。人工林中的父本遗传多样性与远交水平均高于自然块菌林地，这或许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。然而，人工林与自然种群之间并未出现遗传隔离，因此黑孢块菌代表了驯化早期阶段的类群——其遗传结构尚未受到驯化活动的显著影响。