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The Birth of a Black Rice Gene and Its Local Spread by Introgression

Tetsuo Oikawa, Hiroaki Maeda, Taichi Oguchi, Takuya Yamaguchi, Noriko Tanabe, Kaworu Ebana, Masahiro Yano, Takeshi Ebitani, Takeshi Izawa
Tetsuo Oikawa
Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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Hiroaki Maeda
Toyama Prefectural Agricultural, Forestry and Fisheries Research Center, Toyama, Toyama 939-8153, Japan
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Taichi Oguchi
Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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Takuya Yamaguchi
Toyama Prefectural Agricultural, Forestry and Fisheries Research Center, Toyama, Toyama 939-8153, Japan
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Noriko Tanabe
Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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Kaworu Ebana
Rice Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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Masahiro Yano
Rice Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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Takeshi Ebitani
Toyama Prefectural Agricultural, Forestry and Fisheries Research Center, Toyama, Toyama 939-8153, Japan
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  • ORCID record for Takeshi Ebitani
Takeshi Izawa
Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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  • For correspondence: tizawa@affrc.go.jp

Published September 2015. DOI: https://doi.org/10.1105/tpc.15.00310

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  • © 2015 American Society of Plant Biologists. All rights reserved.

Abstract

The origin and spread of novel agronomic traits during crop domestication are complex events in plant evolution. Wild rice (Oryza rufipogon) has red grains due to the accumulation of proanthocyanidins, whereas most cultivated rice (Oryza sativa) varieties have white grains induced by a defective allele in the Rc basic helix-loop-helix (bHLH) gene. Although the events surrounding the origin and spread of black rice traits remain unknown, varieties with black grains due to anthocyanin accumulation are distributed in various locations throughout Asia. Here, we show that the black grain trait originated from ectopic expression of the Kala4 bHLH gene due to rearrangement in the promoter region. Both the Rc and Kala4 genes activate upstream flavonol biosynthesis genes, such as chalcone synthase and dihydroflavonol-4-reductase, and downstream genes, such as leucoanthocyanidin reductase and leucoanthocyanidin dioxygenase, to produce the respective specific pigments. Genome analysis of 21 black rice varieties as well as red- and white-grained landraces demonstrated that black rice arose in tropical japonica and its subsequent spread to the indica subspecies can be attributed to the causal alleles of Kala4. The relatively small size of genomic fragments of tropical japonica origin in some indica varieties indicates that refined introgression must have occurred by natural crossbreeding in the course of evolution of the black trait in rice.

  • Glossary

    bHLH
    basic helix-loop-helix
    FNP
    functional nucleotide polymorphism
    SSR
    simple sequence repeat
    McrBC-CGH
    McrBC-comparative genomic hybridization
    FPNI
    fusion primer and nested integrated
    SNP
    single nucleotide polymorphism
    ORF
    open reading frame
    • Received April 10, 2015.
    • Revised August 14, 2015.
    • Accepted August 26, 2015.
    • Published September 11, 2015.
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    The Birth of a Black Rice Gene and Its Local Spread by Introgression
    Tetsuo Oikawa, Hiroaki Maeda, Taichi Oguchi, Takuya Yamaguchi, Noriko Tanabe, Kaworu Ebana, Masahiro Yano, Takeshi Ebitani, Takeshi Izawa
    The Plant Cell Sep 2015, 27 (9) 2401-2414; DOI: 10.1105/tpc.15.00310

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    The Birth of a Black Rice Gene and Its Local Spread by Introgression
    Tetsuo Oikawa, Hiroaki Maeda, Taichi Oguchi, Takuya Yamaguchi, Noriko Tanabe, Kaworu Ebana, Masahiro Yano, Takeshi Ebitani, Takeshi Izawa
    The Plant Cell Sep 2015, 27 (9) 2401-2414; DOI: 10.1105/tpc.15.00310
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