Journal of Plant Research

, Volume 132, Issue 4, pp 541–568 | Cite as

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

  • Kazunori SakamotoEmail author
  • Natsuko Ogiwara
  • Tomomitsu Kaji
  • Yurie Sugimoto
  • Mitsuru Ueno
  • Masatoshi Sonoda
  • Akihiro Matsui
  • Junko Ishida
  • Maho Tanaka
  • Yasushi Totoki
  • Kazuo Shinozaki
  • Motoaki Seki
Regular Paper


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.


Arbuscular mycorrhizal fungi Dual symbiosis Glycine max Rhizobia Soybean Transcriptome 



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.


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.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Supplementary material

10265_2019_1117_MOESM1_ESM.pdf (522 kb)
Supplementary material 1 (PDF 522 kb)


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Copyright information

© The Botanical Society of Japan and Springer Japan KK, part of Springer Nature 2019

Authors and Affiliations

  • Kazunori Sakamoto
    • 1
    Email author
  • Natsuko Ogiwara
    • 1
  • Tomomitsu Kaji
    • 2
  • Yurie Sugimoto
    • 1
  • Mitsuru Ueno
    • 1
  • Masatoshi Sonoda
    • 1
  • Akihiro Matsui
    • 3
    • 4
  • Junko Ishida
    • 3
    • 4
  • Maho Tanaka
    • 3
    • 4
  • Yasushi Totoki
    • 5
  • Kazuo Shinozaki
    • 3
  • Motoaki Seki
    • 3
    • 4
    • 6
  1. 1.Graduate School of HorticultureChiba UniversityMatsudoJapan
  2. 2.JA ZEN-NOH Research and Development CenterHiratsukaJapan
  3. 3.RIKEN Center for Sustainable Resource ScienceYokohamaJapan
  4. 4.RIKEN Cluster for Pioneering ResearchWakoJapan
  5. 5.Division of Cancer GenomicsNational Cancer Center Research InstituteTokyoJapan
  6. 6.Kihara Institute for Biological ResearchYokohama City UniversityYokohamaJapan

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