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Transcriptome analysis of soybean (Glycine max) root genes differentially expressed in rhizobial, arbuscular mycorrhizal, and dual symbiosis

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Abstract

Soybean (Glycine max) roots establish associations with nodule-inducing rhizobia and arbuscular mycorrhizal (AM) fungi. Both rhizobia and AM fungi have been shown to affect the activity of and colonization by the other, and their interactions can be detected within host plants. Here, we report the transcription profiles of genes differentially expressed in soybean roots in the presence of rhizobial, AM, or rhizobial–AM dual symbiosis, compared with those in control (uninoculated) roots. Following inoculation, soybean plants were grown in a glasshouse for 6 weeks; thereafter their root transcriptomes were analyzed using an oligo DNA microarray. Among the four treatments, the root nodule number and host plant growth were highest in plants with dual symbiosis. We observed that the expression of 187, 441, and 548 host genes was up-regulated and 119, 1,439, and 1,298 host genes were down-regulated during rhizobial, AM, and dual symbiosis, respectively. The expression of 34 host genes was up-regulated in each of the three symbioses. These 34 genes encoded several membrane transporters, type 1 metallothionein, and transcription factors in the MYB and bHLH families. We identified 56 host genes that were specifically up-regulated during dual symbiosis. These genes encoded several nodulin proteins, phenylpropanoid metabolism-related proteins, and carbonic anhydrase. The nodulin genes up-regulated by the AM fungal colonization probably led to the observed increases in root nodule number and host plant growth. Some other nodulin genes were down-regulated specifically during AM symbiosis. Based on the results above, we suggest that the contribution of AM fungal colonization is crucial to biological N2-fixation and host growth in soybean with rhizobial-AM dual symbiosis.

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Acknowledgements

We thank Dr. Ryo Yamamoto (National Agriculture and Food Research Organization, Japan) for providing soybean seeds, and Dr. Taishi Umezawa (Tokyo University of Agriculture and Technology, Japan) for technical assistance.

Funding

This work was supported by Japan Society for the Promotion of Science (JSPS KAKENHI, Grant Number 23380042) to KS; the Japan Science and Technology Agency (JST), Core Research for Evolutionary Science and Technology (CREST) and Grants from RIKEN to MS.

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Authors and Affiliations

  1. Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan

    Kazunori Sakamoto, Natsuko Ogiwara, Yurie Sugimoto, Mitsuru Ueno & Masatoshi Sonoda

  2. JA ZEN-NOH Research and Development Center, 4-18-1 Higashiyawata, Hiratsuka, Kanagawa, 254-0016, Japan

    Tomomitsu Kaji

  3. RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan

    Akihiro Matsui, Junko Ishida, Maho Tanaka, Kazuo Shinozaki & Motoaki Seki

  4. RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan

    Akihiro Matsui, Junko Ishida, Maho Tanaka & Motoaki Seki

  5. Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan

    Yasushi Totoki

  6. Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan

    Motoaki Seki

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  1. Kazunori Sakamoto
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Sakamoto, K., Ogiwara, N., Kaji, T. et al. Transcriptome analysis of soybean (Glycine max) root genes differentially expressed in rhizobial, arbuscular mycorrhizal, and dual symbiosis. J Plant Res 132, 541–568 (2019). https://doi.org/10.1007/s10265-019-01117-7

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