Genome-wide genetic changes during modern breeding of maize

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  • A Corrigendum to this article was published on 27 August 2014

Abstract

The success of modern maize breeding has been demonstrated by remarkable increases in productivity over the last four decades. However, the underlying genetic changes correlated with these gains remain largely unknown. We report here the sequencing of 278 temperate maize inbred lines from different stages of breeding history, including deep resequencing of 4 lines with known pedigree information. The results show that modern breeding has introduced highly dynamic genetic changes into the maize genome. Artificial selection has affected thousands of targets, including genes and non-genic regions, leading to a reduction in nucleotide diversity and an increase in the proportion of rare alleles. Genetic changes during breeding happen rapidly, with extensive variation (SNPs, indels and copy-number variants (CNVs)) occurring, even within identity-by-descent regions. Our genome-wide assessment of genetic changes during modern maize breeding provides new strategies as well as practical targets for future crop breeding and biotechnology.

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Figure 1: GWAS results for cob color.
Figure 2: Neighbor-joining tree of the 126 US maize inbred lines.
Figure 3: CLR and genetic diversity of chromosome 1 in public US, Ex-PVP and elite Chinese maize groups.
Figure 4: The percentage of rare alleles in four related inbred lines.

Accession codes

Primary accessions

NCBI Reference Sequence

Sequence Read Archive

Change history

  • 27 August 2014

    In the version of this article initially published, Figure 2 and related results were flawed because of errors in the analysis that incorrectly assigned the B73 reference genotype to non–overlapping SNP sites, resulting in SNPs being inappropriately combined. In addition, the authors have revised identity–by–descent (IBD) region identification using a 50–SNP sliding window with a step size of 5 SNPs and excluded regions with genetic distance of ≤0.05 cM. As a result of these changes, the authors have provided a corrected version of the paper to be appended to the original publication (the Online Methods, Figs. 1–4 and their legends, and Table 1 and its legend were revised). Minor revisions have also been made in the main text to reflect changes to calculations resulting from the above corrections (changes are made in paragraphs 2 and 3 of original page 812, paragraphs 1 and 2 of original page 813, and paragraphs 1–6 of original page 814). In addition, corrected versions of Supplementary Tables 2–6 and 11 and Supplementary Figures 1, 2, 5 and 6, and two new supplementary figures and one new supplementary table have been added. The main conclusions of the paper were not affected by the corrections.

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Acknowledgements

We thank E.S. Buckler and J. Ross-Ibarra for helpful discussions, E.S. Buckler, T.R. Rocheford, M. Bohn and P. Becraft for assistance in making some of the Ex-PVP lines available and J. Dai, S. Wang and T. Wang for sharing Chinese germplasm. Research is supported by the National Basic Research Program (973 program) (2009CB118400).

Author information

J.L. designed the project. J.L., Y.J. and H.Z. wrote the manuscript. Y.J., H.Z., L.R., B.Z. and S.X. performed most data analyses. W.S., J.G., B.W., Z.L., J.C., W.L. and M.Z. collected the inbred lines and prepared DNA samples for sequencing.

Correspondence to Jinsheng Lai.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–4 and 6–11 and Supplementary Figures 1–8 (PDF 918 kb)

Supplementary Table 5

The list of selective regions and genes (XLSX 524 kb)

Supplementary Table 12

Three subgroups of the 278 inbred lines (XLSX 19 kb)

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