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 a 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.

食用菌的生活史与传播机制至今仍鲜有系统研究，这极大限制了学界对其演化与驯化进程的认知。备受推崇的黑孢块菌（Tuber melanosporum）可形成子实体（fruitbody，即减数孢子成熟的肉质产孢器官），其野生资源可于自然接种的原生林中采集，人工栽培产品则可在苗圃接种苗木营造的人工林内收获。然而，子实体的形成机制至今仍不明晰，这直接制约了块菌产量的提升；同时，当前驯化实践如何影响种群遗传结构的关键问题也尚未得到关注。子实体源于两个单倍体个体的交配过程：母本负责构建肉质组织并产生减数孢子，而父本仅参与减数孢子的形成。本研究以法国东南部的950份样本为材料，利用简单序列重复（Simple Sequence Repeat, SSR）多态性位点，对原生林与人工林内的黑孢块菌种群遗传多样性开展了对比分析。结果显示，所有种群均在空间尺度上表现出显著的距离隔离效应，这可能源于动物介导的孢子传播、减数孢子在土壤中的长期留存，以及营养体不亲和性对非亲缘个体的排斥作用。研究始终检测到较高水平的近交现象，这表明亲本往往源自同一子实体产生的减数孢子。与母本基因型不同，父本菌丝体仅能参与形成少量子实体，且无法跨年度存活，同时在林木菌根（mycorrhiza）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配偶体参与交配。人工林内的父本遗传多样性与远交率均显著高于原生块菌林地，这可能是因为块菌种植者通过人工散播子实体来维持人工林的接种效果。但值得注意的是，人工种群与原生种群并未出现遗传分化，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。