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Genome-wide patterns of genetic variation among elite maize inbred lines

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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Figure 1: Genetic background of three sequenced inbred lines.
Figure 2: Annotation of large-effect SNPs.
Figure 3: Genome-wide distribution of sequence diversity level, gene density, zero-diversity genes and selected genes on chromosome 4.
Figure 4: Numbers of PAVs relative to the B73 reference genome.

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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.

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Authors

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.

Corresponding authors

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

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The authors declare no competing financial interests.

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Supplementary Figures 1–3 and Supplementary Tables 1–5 (PDF 2815 kb)

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Lai, J., Li, R., Xu, X. et al. Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42, 1027–1030 (2010). https://doi.org/10.1038/ng.684

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