Corrigendum: Genome-wide genetic changes during modern breeding of maize

Nat. Genet. 44, 812–815 (2012); published online 3 June 2012; corrected after print 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.

Nat. Genet. 44, 812–815 (2012); published online 3 June 2012; corrected after print 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. 1,2,3,4 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 2–4,5,6 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.

Figure 1: GWAS results for cob color.

(a) Manhattan plot. (b) Quantile-quantile plot. (c) Regional Manhattan plot of 5 Mb on either side of the peak SNP.

Figure 2: Neighbor-joining tree of the 126 US maize inbred lines.

Lines in the public US group are shown in red followed by an asterisk. Ex-PVP lines are shown in black.

Figure 3: CLR and genetic diversity of chromosome 1 in public US, Ex-PVP and elite Chinese maize groups.

Green lines, public US group; blue lines, Ex-PVP group; red lines, elite Chinese group; orange lines, F_ST of the Chinese and US (both public and Ex-PVP) maize groups; purple lines, F_ST of the public US group and Ex-PVP groups.

Figure 4: The percentage of rare alleles in four related inbred lines.

Allele frequencies were calculated in the 278 Chinese and US lines. Rare alleles are defined as those present in ≤5% of the sequenced lines. B73 is known to be the ancestral line of 8112, 478 and Zheng58. All share the Iowa Stiff Stalk background.

Table 1 Mutation rates of base substitutions, short indels and copy number variations