Plant Molecular Biology

, Volume 64, Issue 4, pp 467–479 | Cite as

Structural features of GmIRCHS, candidate of the I gene inhibiting seed coat pigmentation in soybean: implications for inducing endogenous RNA silencing of chalcone synthase genes

  • Atsushi Kasai
  • Kosuke Kasai
  • Setsuzo Yumoto
  • Mineo Senda


Most commercial soybean varieties have yellow seeds due to loss of pigmentation in the seed coat. The I gene inhibits pigmentation over the entire seed coat, resulting in a uniform yellow color of mature harvested seeds. We previously demonstrated that the inhibition of seed coat pigmentation by the I gene results from post-transcriptional gene silencing (PTGS) of chalcone synthase (CHS) genes. Little is known about the structure of the I gene and the mechanism by which it induces PTGS of CHS genes. Here, we report a candidate of the I gene, GmIRCHS, which consists of a 5′-portion of a DnaJ-like gene containing a promoter region and a perfect inverted repeat (IR) of 1.1-kb truncated CHS3 sequences (5′-ΔCHS3 and 3′-ΔCHS3). RT-PCRs and RNase protection assay indicated the existence of the read-through product from 5′-ΔCHS3 to 3′-ΔCHS3 and the dsRNA region of ΔCHS3, suggesting that dsRNA of ΔCHS3 could be transcribed from GmIRCHS and could induce PTGS of CHS genes. Moreover, the IR structure of ΔCHS3 in GmIRCHS was lost in the soybean mutants in which I was changed to i, supporting the conclusion that GmIRCHS is the I gene.


CHS genes Endogenous RNA silencing I gene Inverted repeat Seed coat Soybean 



Chalcone synthase


Double-stranded RNA


Inverted repeat


Open reading frame


Post-transcriptional gene silencing


Rapid amplification of cDNA ends


RNA-directed RNA polymerase


Restriction fragment length polymorphism


RNA interference


Reverse transcription


Short interfering RNA


Untranslated region



This work was supported in part by Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan, and from Hirosaki University (Priority Area, 2003–2006), Japan, and a research grant from the Iijima Memorial Foundation for the Promotion of Food Science and Technology, Japan.


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Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Atsushi Kasai
    • 1
  • Kosuke Kasai
    • 2
  • Setsuzo Yumoto
    • 3
    • 4
  • Mineo Senda
    • 1
  1. 1.Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiJapan
  2. 2.Department of Medical TechnologyHirosaki University School of Health SciencesHirosakiJapan
  3. 3.Hokkaido Prefectural Tokachi Agricultural Experiment StationKasai-gunJapan
  4. 4.Soybean Breeding Research SubteamNational Agricultural Research Center for Tohoku RegionDaisenJapan

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