Abstract

We have resequenced a group of six elite maize inbred lines, including the parents of the most productive commercial hybrid in China. This effort uncovered more than 1,000,000 SNPs, 30,000 indel polymorphisms and 101 low-sequence-diversity chromosomal intervals in the maize genome. We also identified several hundred complete genes that show presence/absence variation among these resequenced lines. We discuss the potential roles of complementation of presence/absence variations and other deleterious mutations in contributing to heterosis. High-density SNP and indel polymorphism markers reported here are expected to be a valuable resource for future genetic studies and the molecular breeding of this important crop.

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Acknowledgements

Supported by the 973 program (2009CB118400; 2007CB815703; 2007CB815705; 2007CB109000), the 863 project (2010AA10A106), the National Natural Science Foundation of China (30725008), the Shenzhen Bureau of Science Technology & Information, China (ZYC200903240077A; CXB200903110066A), the Chinese Academy of Science (GJHZ0701-6), the Ole Rømer grant from the Danish Natural Science Research Council and the US National Science Foundation (DBI-0527192). We thank L. Goodman for editing the manuscript.

Author information

Author notes

    • Jinsheng Lai
    • , Ruiqiang Li
    • , Xun Xu
    • , Weiwei Jin
    •  & Mingliang Xu

    These authors contributed equally to this work.

Affiliations

  1. State Key Lab of Agrobiotechnology, China Agricultural University, Beijing, China.

    • Jinsheng Lai
    • , Hainan Zhao
    • , Zhongkai Xiang
    • , Weibin Song
    • , Mei Zhang
    •  & Yinping Jiao
  2. National Maize Improvement Center, China Agricultural University, Beijing, China.

    • Jinsheng Lai
    • , Weiwei Jin
    • , Mingliang Xu
    • , Hainan Zhao
    • , Zhongkai Xiang
    • , Weibin Song
    • , Mei Zhang
    • , Yinping Jiao
    • , Shoucai Wang
    • , Shaojiang Chen
    • , Jiansheng Li
    •  & Jingrui Dai
  3. BGI-Shenzhen, Shenzhen, China.

    • Ruiqiang Li
    • , Xun Xu
    • , Peixiang Ni
    • , Jianguo Zhang
    • , Dong Li
    • , Xiaosen Guo
    • , Kaixiong Ye
    • , Min Jian
    • , Bo Wang
    • , Huisong Zheng
    • , Huiqing Liang
    • , Xiuqing Zhang
    • , Huanming Yang
    • , Jian Wang
    •  & Jun Wang
  4. Center for Plant Genomics, Iowa State University, Ames, Iowa, USA.

    • Kai Ying
    • , Yan Fu
    •  & Patrick S Schnable
  5. Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, USA.

    • Nathan M Springer
  6. Department of Biology, University of Copenhagen, Copenhagen, Denmark.

    • Jun Wang

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Contributions

J. Lai, Jun Wang, R.L., J.D. and P.S.S. managed the project. X.X., H. Zhao, Z.X., W.S., M.Z., Y.J., P.N., M.J., B.W., H. Zheng, H.L. and X.Z. performed experiments and sequencing. J. Lai, Jun Wang, R.L., X.X., Jian Wang and H.Y. designed the analyses. X.X., R.L., W.J., M.X., K. Ying, J.Z., D.L., X.G., K. Ye, S.W., S.C., J. Li and Y.F. performed data analyses. J. Lai, P.S.S., N.M.S., Jun Wang, K. Ying and X.X. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Jinsheng Lai or Patrick S Schnable or Jun Wang.

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DOI

https://doi.org/10.1038/ng.684

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