Deletion in a gene associated with grain size increased yields during rice domestication (original) (raw)

Nature Genetics volume 40, pages 1023–1028 (2008)Cite this article

Abstract

The domestication of crops involves a complex process of selection in plant evolution and is associated with changes in the DNA regulating agronomically important traits. Here we report the cloning of a newly identified QTL, qSW5 (QTL for seed width on chromosome 5), involved in the determination of grain width in rice. Through fine mapping, complementation testing and association analysis, we found that a deletion in qSW5 resulted in a significant increase in sink size owing to an increase in cell number in the outer glume of the rice flower; this trait might have been selected by ancient humans to increase yield of rice grains. In addition, we mapped two other defective functional nucleotide polymorphisms of rice domestication-related genes with genome-wide RFLP polymorphisms of various rice landraces. These analyses show that the qSW5 deletion had an important historical role in artificial selection, propagation of cultivation and natural crossings in rice domestication, and shed light on how the rice genome was domesticated.

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Acknowledgements

We thank H. Kanamori of Institute of the Society for Techno-Innovation of Agriculture, Forestry and Fisheries and T. Matsumoto of National Institute of Agrobiological Sciences for genomic sequencing of the qSW5 region of Kasalath, Y. Kojima for RFLP data production, and K. Ono for Kasalath transformation. M.Y. was supported by MP1113 (Integrated research project for plant, insect and animal using genome technology) and T.I. has been supported by GD2008 (Integrated research project for plant, insect and animal using genome technology) and QTL5001 (Genomics for Agricultural Innovation) of the Ministry of Agriculture, Forestry and Fisheries of Japan.

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Author notes

  1. Ayahiko Shomura and Takeshi Izawa: These authors contributed equally to this work.

Authors and Affiliations

  1. Institute of the Society for Techno-Innovation of Agriculture, Forestry, and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, 305-0854, Ibaraki, Japan
    Ayahiko Shomura
  2. Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, 305-8602, Ibaraki, Japan
    Takeshi Izawa & Saeko Konishi
  3. QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, 305-8602, Ibaraki, Japan
    Kaworu Ebana, Hiromi Kanegae & Masahiro Yano
  4. Toyama Agricultural Research Center, 1124-1, Yoshioka, 939-8153, Toyama, Japan
    Takeshi Ebitani

Authors

  1. Ayahiko Shomura
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  2. Takeshi Izawa
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  3. Kaworu Ebana
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  4. Takeshi Ebitani
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  5. Hiromi Kanegae
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  6. Saeko Konishi
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  7. Masahiro Yano
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Contributions

A.S. performed most of the experiments. S.K. helped A.S. with the experiments and carried out qRT-PCR expression analysis. H.K. performed the original QTL analysis with the F2 population. T.E. field-tested NIL(qSW5). K.E. provided genome-wide RFLP data on rice landraces. M.Y. directed the QTL analysis, material production and fine mapping of qSW5. T.I. directed the research, designed the experiments for all the other parts and analyzed the FNPs with genome data, and wrote the manuscript. All authors contributed to improve the manuscript.

Corresponding author

Correspondence toTakeshi Izawa.

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Shomura, A., Izawa, T., Ebana, K. et al. Deletion in a gene associated with grain size increased yields during rice domestication.Nat Genet 40, 1023–1028 (2008). https://doi.org/10.1038/ng.169

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