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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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References

  1. SanMiguel, P. et al. Nested retrotransposons in the intergenic regions of the maize genome. Science 274, 765–768 (1996).

    Article  CAS  PubMed  Google Scholar 

  2. Messing, J. et al. Sequence composition and genome organization of maize. Proc. Natl. Acad. Sci. USA 101, 14349–14354 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Whitelaw, C.A. et al. Enrichment of gene-coding sequences in maize by genome filtration. Science 302, 2118–2120 (2003).

    Article  PubMed  Google Scholar 

  4. Palmer, L.E. et al. Maize genome sequencing by methylation filtration. Science 302, 2115–2117 (2003).

    Article  PubMed  Google Scholar 

  5. Tenaillon, M.I. et al. Patterns of diversity and recombination along chromosome 1 of maize (Zea mays ssp. mays L.). Genetics 162, 1401–1413 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Tenaillon, M.I. et al. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc. Natl. Acad. Sci. USA 98, 9161–9166 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Wang, J. et al. The diploid genome sequence of an Asian individual. Nature 456, 60–65 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Wheeler, D.A. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872–876 (2008).

    Article  CAS  PubMed  Google Scholar 

  9. Schnable, P.S. et al. The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112–1115 (2009).

    Article  CAS  PubMed  Google Scholar 

  10. Li, R., Li, Y., Kristiansen, K. & Wang, J. SOAP: short oligonucleotide alignment program. Bioinformatics 24, 713–714 (2008).

    Article  CAS  PubMed  Google Scholar 

  11. Li, R. et al. SNP detection for massively parallel whole-genome resequencing. Genome Res. 19, 1124–1132 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Watterson, G.A. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7, 256–276 (1975).

    Article  CAS  PubMed  Google Scholar 

  13. Gore, M.A. et al. A first-generation haplotype map of maize. Science 326, 1115–1117 (2009).

    Article  CAS  PubMed  Google Scholar 

  14. Clark, R.M. et al. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317, 338–342 (2007).

    Article  CAS  PubMed  Google Scholar 

  15. Bakker, E.G., Toomajian, C., Kreitman, M. & Bergelson, J. A genome-wide survey of R gene polymorphisms in Arabidopsis. Plant Cell 18, 1803–1818 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Grant, M.R. et al. Independent deletions of a pathogen-resistance gene in Brassica and Arabidopsis. Proc. Natl. Acad. Sci. USA 95, 15843–15848 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Whitt, S.R., Wilson, L.M., Tenaillon, M.I., Gaut, B.S. & Buckler, E.S. IV. Genetic diversity and selection in the maize starch pathway. Proc. Natl. Acad. Sci. USA 99, 12959–12962 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Wright, S.I. et al. The effects of artificial selection on the maize genome. Science 308, 1310–1314 (2005).

    Article  CAS  PubMed  Google Scholar 

  19. Fu, H. & Dooner, H.K. Intraspecific violation of genetic colinearity and its implications in maize. Proc. Natl. Acad. Sci. USA 99, 9573–9578 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Lai, J., Li, Y., Messing, J. & Dooner, H.K. Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc. Natl. Acad. Sci. USA 102, 9068–9073 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Morgante, M. et al. Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat. Genet. 37, 997–1002 (2005).

    Article  CAS  PubMed  Google Scholar 

  22. Springer, N.M. et al. Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet. 5, e1000734 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  23. Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272 (2009).

    Article  PubMed  Google Scholar 

  24. Quevillon, E. et al. InterProScan: protein domains identifier. Nucleic Acids Res. 33, W116–120 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Springer, N.M. & Stupar, R.M. Allelic variation and heterosis in maize: how do two halves make more than a whole? Genome Res. 17, 264–275 (2007).

    Article  CAS  PubMed  Google Scholar 

  26. Charlesworth, D. & Willis, J.H. The genetics of inbreeding depression. Nat. Rev. Genet. 10, 783–796 (2009).

    Article  CAS  PubMed  Google Scholar 

  27. McMullen, M.D. et al. Genetic properties of the maize nested association mapping population. Science 325, 737–740 (2009).

    Article  CAS  PubMed  Google Scholar 

  28. Tajima, F. Evolutionary relationship of DNA sequences in finite populations. Genetics 105, 437–460 (1983).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Xia, Q. et al. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 326, 433–436 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res. 14, 988–995 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Everitt, B.S. An introduction to finite mixture distributions. Stat. Methods Med. Res. 5, 107–127 (1996).

    Article  CAS  PubMed  Google Scholar 

  32. Dempster, A.P., Laird, N.M. & Rubin, D.B. Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. (Ser. A) 39, 1–38 (1977).

    Google Scholar 

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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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