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Genotypic diversity of the Asiatic black truffle, Tuber himalayense, collected in spontaneous and highly productive truffle grounds

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Abstract

Tuber himalayense is a species of edible Asiatic black truffle which is sister to Tuber indicum. Local populations contribute significantly to the reproduction of truffles, but fundamental data of fine-scale genetic structure is lacking in Asiatic truffle species. In this study, we provide the first report on the genotypic diversity and spatial fruiting pattern of an Asiatic truffle T. himalayense, in two spontaneous productive truffle grounds 140 m apart from one another in Yamanashi, Japan. Ascocarps were collected from 2004 to 2009 and in 2011. The spatial distribution of samples was recorded and genotypic diversity of the fungal individuals was examined using 15 newly developed and 4 existing simple sequence repeat (SSR) markers. The spatial distribution analyses suggested non-random, year-specific aggregation patterns of ascocarps in both plots. However, no consistent tendency was observed across the entire sampling period, with fruiting positions showing neither an obvious expansion nor a steady displacement. Although only a single SSR genotype, representing one gleba-forming maternal individual, was detected, the genotype was further divided into two different mating types, suggesting multiple, closely related individuals that were indistinguishable using the SSR analysis. The results indicated strong founding effects along with high inbreeding within populations, likely due to the limited dispersal opportunities into these sites. Despite low genetic diversity in the truffle grounds, the plots remained productive over the sampling years, indicating that low genetic diversity does not necessarily have an adverse effect on truffle production, at least not during a period of several years.

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Data availability

The datasets and codes generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

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Acknowledgments

We thank Mr. Masaru Ohkubo, Mr. Taisuke Kamiya and Mr. Yusuke Aikawa for helping and collecting. We also thank Dr. Mitsuteru Akiba and Dr. Asako Matsumoto of FFPRI for their helpful advices on the SSR analysis.

Funding

This work was financially supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan entitled “Technology development for the optimal use of forest resources.”

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Authors and Affiliations

  1. Department of Mushroom Science and Forest Microbiology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Matsunosato 1, Tsukuba, Ibaraki, 305-8687, Japan

    Noritaka Nakamura, Akihiko Kinoshita, Keisuke Obase, James Raymond Peter Worth, Shota Nakano & Takashi Yamanaka

  2. Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan

    Junichi Peter Abe

  3. Yamanashi Forestry and Forest Products Research Institute, Yamanashi, Japan

    Hisashi Shibata

  4. College of Bioresource Sciences, Nihon University, Tokyo, Japan

    Yuko Ota

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  1. Noritaka Nakamura
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  2. Junichi Peter Abe
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  3. Hisashi Shibata
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  4. Akihiko Kinoshita
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Contributions

This study was conceptualized by JPA and TY. Field study was performed by JPA and HS. Ascocarp samples were collected by AK from various locations in Japan. Molecular markers were developed and tested by KO, JRPW, YO, and NN. Molecular and spatial analyses were performed by NN. The first draft of the manuscript was written by NN and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Noritaka Nakamura.

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Supplementary Figure 1

Spatial distribution of fruiting positions in the plots of Quercus dentata (a) and Castanea crenata (b). Colors and symbols correspond to sampling years. Filled circles represent trees. (PDF 74 kb)

Supplementary Figure 2

Frequency of distances between ascocarps and its nearest trees in the plots of Quercus dentata (a) and Castanea crenata (b). (PDF 27 kb)

Supplementary Figure 3

L(r) values of the spatial distribution of the fruiting positions in 2004 (a), 2005 (b), 2006 (c), 2007 (d), 2008 (e), 2009 (f) and 2011 (g) in the plot of Quercus dentata and 2007 (h), 2008 (i), 2009 (j) and 2011 (k) in the plot of Castanea crenata. The 99% confidence simulation envelopes are shown as gray, shaded regions. L(r) values outside of the confidence envelopes indicate significant deviation from random distribution, with higher values indicating aggregation and lower values dispersion. (PDF 180 kb)

Supplementary Figure 4

Spatial distribution of fruiting positions and fruiting clusters in the plots of Quercus dentata (a) and Castanea crenata (b). Colors correspond to sampling years. Localities of fruiting clusters are shown in triangles. Filled circles represent trees. (PDF 91 kb)

Supplementary Figure 5

Spatial distribution of the ascocarps in the plots of Quercus dentata (a) and Castanea crenata (b), which were used for molecular analyses. Gray symbols represent samples where simple sequence repeat-multilocus genotypes (SSR-MLG) failed to be determined for at least one of all 19 loci. The remaining samples in both plots represent the identical SSR-MLG. Filled circles represent trees. (PDF 32 kb)

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Nakamura, N., Abe, J.P., Shibata, H. et al. Genotypic diversity of the Asiatic black truffle, Tuber himalayense, collected in spontaneous and highly productive truffle grounds. Mycol Progress 19, 1511–1523 (2020). https://doi.org/10.1007/s11557-020-01642-z

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