Abstract

A key step during crop domestication is the loss of seed shattering. Here, we show that seed shattering in sorghum is controlled by a single gene, Shattering1 (Sh1), which encodes a YABBY transcription factor. Domesticated sorghums harbor three different mutations at the Sh1 locus. Variants at regulatory sites in the promoter and intronic regions lead to a low level of expression, a 2.2-kb deletion causes a truncated transcript that lacks exons 2 and 3, and a GT-to-GG splice-site variant in the intron 4 results in removal of the exon 4. The distributions of these non-shattering haplotypes among sorghum landraces suggest three independent origins. The function of the rice ortholog (OsSh1) was subsequently validated with a shattering-resistant mutant, and two maize orthologs (ZmSh1-1 and ZmSh1-5.1+ZmSh1-5.2) were verified with a large mapping population. Our results indicate that Sh1 genes for seed shattering were under parallel selection during sorghum, rice and maize domestication.

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Acknowledgements

This work was supported by an Agriculture and Food Research Initiative Competitive Grant (2011-03587 to J.Y. and T.T.T.) from the US Department of Agriculture (USDA) National Institute of Food and Agriculture, the Plant Genome Research Program of the National Science Foundation (DBI-0820610 to J.Y., DBI-0820619 to J.D. and DBI-1027527 to P.S.S.), the Plant Feedstock Genomics Program of the US Department of Energy (DE-SC0002259 to J.Y.), the USDA-ARS (M.L.W. and G.B.), the Targeted Excellence Program of Kansas State University and the Kansas State University Center for Sorghum Improvement.

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Affiliations

  1. Department of Agronomy, Kansas State University, Manhattan, Kansas, USA.

    • Zhongwei Lin
    • , Xianran Li
    • , Guihua Bai
    • , Tesfaye T Tesso
    •  & Jianming Yu
  2. Department of Genetics, University of Wisconsin, Madison, Wisconsin, USA.

    • Laura M Shannon
    •  & John Doebley
  3. Center for Plant Genomics, Iowa State University, Ames, Iowa, USA.

    • Cheng-Ting Yeh
    •  & Patrick S Schnable
  4. Department of Agronomy, Iowa State University, Ames, Iowa, USA.

    • Cheng-Ting Yeh
    •  & Patrick S Schnable
  5. US Department of Agriculture–Agricultural Research Service (USDA-ARS), Griffin, Georgia, USA.

    • Ming L Wang
  6. USDA-ARS, Manhattan, Kansas, USA.

    • Guihua Bai
  7. Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA.

    • Zhao Peng
    • , Jiarui Li
    • , Harold N Trick
    •  & Frank White
  8. Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska, USA.

    • Thomas E Clemente
  9. Department of Agronomy, Purdue University, West Lafayette, Indiana, USA.

    • Mitchell R Tuinstra

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Contributions

J.Y., F.W., T.T.T. and M.R.T. designed research. Z.L., X.L., L.M.S., C.-T.Y., Z.P. and J.L. carried out the research. M.L.W., G.B., H.N.T., T.E.C., J.D. and P.S.S. contributed new reagents. Z.L., X.L., L.M.S. and C.-T.Y. analyzed data. Z.L. and J.Y. wrote the manuscript with input from all other coauthors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jianming Yu.

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    Supplementary Figures 1–4, Supplementary Tables 1–7 and Supplementary Note

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    Supplementary Table 8

    Predicted genes in the syntenic block in sorghum, rice, maize, and foxtail millet

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DOI

https://doi.org/10.1038/ng.2281

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