Reduction in seed shattering was an important phenotypic change during cereal domestication1,2. Here we show that a simple morphological change in rice panicle shape, controlled by the SPR3 locus, has a large impact on seed-shedding and pollinating behaviors. In the wild genetic background of rice, we found that plants with a cultivated-like type of closed panicle had significantly reduced seed shedding through seed retention. In addition, the long awns in closed panicles disturbed the free exposure of anthers and stigmas on the flowering spikelets, resulting in a significant reduction of the outcrossing rate. We localized the SPR3 locus to a 9.3-kb genomic region, and our complementation tests suggest that this region regulates the liguleless gene (OsLG1). Sequencing analysis identified reduced nucleotide diversity and a selective sweep at the SPR3 locus in cultivated rice. Our results suggest that a closed panicle was a selected trait during rice domestication.

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We thank the National Institute of Genetics (National Bioresource Project), Japan, and the National Institute of Agrobiological Sciences, Japan, for providing the seeds of wild and cultivated rice, Y. Takezaki and P.D.T. Phuong for helping with field experiments and H. Fukaki for supporting expression analysis. This work was supported in part by a Grant-in-Aid from Japanese Society for Promotion of Science to T.I. (20580005, 23580006, 23.01390) and by the Japan Science and Technology Agency-Japan International Cooperation Agency within the framework of the Science and Technology Research Partnership for Sustainable Development to M.A.

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  1. Graduate School of Agricultural Science, Kobe University, Kobe, Japan.

    • Takashige Ishii
    • , Koji Numaguchi
    • , Pham Thien Thanh
    • , Than Myint Htun
    • , Masanori Yamasaki
    •  & Ryo Ishikawa
  2. Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan.

    • Kotaro Miura
    • , Norio Komeda
    •  & Motoyuki Ashikari
  3. Faculty of Biotechnology, Fukui Prefectural University, Yoshida, Japan.

    • Kotaro Miura
  4. Iwate Biotechnology Institute, Kitakami, Japan.

    • Kentaro Yoshida
    •  & Ryohei Terauchi
  5. The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.

    • Kentaro Yoshida
  6. National Institute of Agrobiological Sciences, Tsukuba, Japan.

    • Takashi Matsumoto


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T.I., K.N. and P.T.T. performed the field experiments and analyzed the results. T.M.H. and R.I. conducted the histological analysis. T.M. produced constructs, and K.M., N.K., R.I. and M.A. generated and analyzed transformants. K.N., M.Y., K.Y. and R.T. participated in sequence analysis, and T.I. and M.A. designed the research and wrote the manuscript.

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The authors declare no competing financial interests.

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Correspondence to Takashige Ishii.

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