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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

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Abstract

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.

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Abbreviations

CHS:

Chalcone synthase

dsRNA:

Double-stranded RNA

IR:

Inverted repeat

ORF:

Open reading frame

PTGS:

Post-transcriptional gene silencing

RACE:

Rapid amplification of cDNA ends

RDR:

RNA-directed RNA polymerase

RFLP:

Restriction fragment length polymorphism

RNAi:

RNA interference

RT:

Reverse transcription

siRNA:

Short interfering RNA

UTR:

Untranslated region

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Acknowledgements

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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  1. Setsuzo Yumoto

    Present address: Soybean Breeding Research Subteam, National Agricultural Research Center for Tohoku Region, Kariwano, Daisen, Akita, 019-2112, Japan

Authors and Affiliations

  1. Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori, 036-8561, Japan

    Atsushi Kasai & Mineo Senda

  2. Department of Medical Technology, Hirosaki University School of Health Sciences, Hon-cho 66, Hirosaki, Aomori, 036-8564, Japan

    Kosuke Kasai

  3. Hokkaido Prefectural Tokachi Agricultural Experiment Station, S9-2, Shinsei, Memuro-cho, Kasai-gun, Hokkaido, 082-0071, Japan

    Setsuzo Yumoto

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  1. Atsushi Kasai
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Correspondence to Mineo Senda.

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Kasai, A., Kasai, K., Yumoto, S. et al. 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. Plant Mol Biol 64, 467–479 (2007). https://doi.org/10.1007/s11103-007-9169-4

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