NATURE GENETICS CORRECTION NOTICE Nat. Genet. 44, 812–815 (2012); published online 3 June 2012; corrected online 27 August 2014 Genome-wide genetic changes during modern breeding of maize Yinping Jiao, Hainan Zhao, Longhui Ren, Weibin Song, Biao Zeng, Jinjie Guo, Baobao Wang, Zhipeng Liu, Jing Chen, Wei Li, Mei Zhang, Shaojun Xie & Jingsheng Lai In the version of this supplementary file originally posted online, Supplementary Figures 1, 2, 5 and 6 and Supplementary Tables 2–4, 6 and 11 contained errors. Corrected versions of these, as well as two new figures—Supplementary Figures 7 and 8—have been appended to this file as of 27 August 2014. See the article corrigendum for full details.
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NATURE GENETICS
CORRECT ION NOT ICE
Nat. Genet. 44, 812–815 (2012); published online 3 June 2012; corrected online 27 August 2014
Genome-wide genetic changes during modern breeding of maizeYinping Jiao, Hainan Zhao, Longhui Ren, Weibin Song, Biao Zeng, Jinjie Guo, Baobao Wang, Zhipeng Liu, Jing Chen, Wei Li, Mei Zhang, Shaojun Xie & Jingsheng LaiIn the version of this supplementary file originally posted online, Supplementary Figures 1, 2, 5 and 6 and Supplementary Tables 2–4, 6 and 11 contained errors. Corrected versions of these, as well as two new figures—Supplementary Figures 7 and 8—have been appended to this file as of 27 August 2014. See the article corrigendum for full details.
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Supplementary Information
Genome-wide genetic changes during modern breeding of maize
Supplementary Table 3. The top five signals of genome-wide significant association of three traits. Trait Chromosome Position -log10p
Silk color 10 138,090,892 5.96 Silk color 10 138,453,309 5.95 Silk color 10 138,453,348 5.95 Silk color 10 138,461,950 6.16 Silk color 10 138,462,086 6.04
Days to anthesis 4 152,721,073 5.85 Days to anthesis 4 152,733,096 5.93 Days to anthesis 4 152,763,319 6.54 Days to anthesis 4 152,788,672 5.82 Days to anthesis 8 130,749,583 5.75
Cob color 1 47,805,826 18.42 Cob color 1 47,806,960 16.71 Cob color 1 47,807,004 16.71 Cob color 1 47,993,467 17.04 Cob color 1 48,024,206 23.97
Nature Genetics: doi:10.1038/ng.2312
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Supplementary Table 4. Tajima’s D and nucleotide diversity (π) of the three maize groups. Public US lines Ex-PVP lines Elite Chinese lines
D of whole genome -0.46 -0.33 -0.28
D of genic region -0.08 0.13 0.25
D of seletion targets -1.25 -1.70 -1.54
π of whole genome 0.0056 0.0050 0.0055
π of genic region 0.0051 0.0045 0.0050
π of seletion targets 0.0033 0.0019 0.0018
Nature Genetics: doi:10.1038/ng.2312
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Supplementary Table 6. The list of selective target genes with function reported. The highlighted six genes have their function reported in Arabidopsis or rice.
Gene ID Group Annotation GRMZM2G088753 Ex-PVP starch branching enzyme1(sbe1)1 GRMZM2G057116 Ex-PVP WRKY transcription factor 102 GRMZM2G300348 Ex-PVP phytoene synthase (y1)3 GRMZM2G078798 Ex-PVP gibberellin catabolism ga2ox14 GRMZM2G132898 Ex-PVP CTP:phosphorylcholine cytidylyltransferase5 GRMZM2G163242 Ex-PVP Armadillo repeat protein ARO16 GRMZM2G175755 Public US plastid ribosomal protein ZmPRPL35-17 GRMZM2G103881 Public US staygreen protein Sgr8 GRMZM2G123815 Public US grain size 5 GS59 GRMZM2G026939 Public US 19kD alpha zein B110 GRMZM2G123587 Elite Chinese DEMETER11 GRMZM2G420801 Elite Chinese Ethylene receptor12 GRMZM2G121897 Elite Chinese transcription factor subunit NF-YB213 GRMZM5G836729 Elite Chinese PHD finger protein14
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Supplementary Table 7. Summary of deep sequencing of 4 inbred lines.
Supplementary Table 11. Pattern of copy number variation for CNV genes across breeding. Copy numbers of CNV genes were investigated within a pedigree from 5003 and 8112 to 478. Up CNV, genes with copy number in offspring higher than any parents; down CNV, genes with copy number in offspring lower than any parents, Additive CNV, genes with copy number in offspring between that of their two parents.
Genes with CNV between parents
Genes do not shown CNV between parents
Up CNV 98 298 Additive CNV 2,085 - Down CNV 144 227
Total genes with CNV 2,327 525
Nature Genetics: doi:10.1038/ng.2312
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2. Supplementary Figures
Supplementary Figure 1. The GWAS results of silk color and days to anthesis. (a) Manhattan plot of GWAS result for silk color. (b) Quantile-quantile plot of GWAS result for silk color. (c). Regional Manhattan plot of 5Mb around the peak SNP of GWAS result for silk color. (d) Manhattan plot of GWAS result for days to anthesis. (e) Quantile-quantile plot of GWAS result for days to anthesis. (f). Regional Manhattan plot of 5Mb around the peak SNP of GWAS result for days to anthesis.
Nature Genetics: doi:10.1038/ng.2312
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Supplementary Figure 2. CLR and genetic diversity of chromosome 2-10 of three maize inbred groups. Green lines represents public US subgroup, blue lines the Ex-PVP subgroup and dark red lines the Chinese group. Orange lines represents FST of China and US (both public US lines and Ex-PVP lines) maize group, Purple lines represents FST of public US group and Ex-PVP group. CLR and genetic diversity of chromosome 2.
Nature Genetics: doi:10.1038/ng.2312
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Supplementary Figure 2. CLR and genetic diversity of chromosome 2-10 of three maize inbred groups (continue). CLR and genetic diversity of chromosome 3.
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Supplementary Figure 2. CLR and genetic diversity of chromosome 2-10 of three maize inbred groups (continue). CLR and genetic diversity of chromosome 4.
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Supplementary Figure 2. CLR and genetic diversity of chromosome 2-10 of three maize inbred groups (continue). CLR and genetic diversity of chromosome 5.
Nature Genetics: doi:10.1038/ng.2312
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Supplementary Figure 2. CLR and genetic diversity of chromosome 2-10 of three maize inbred groups (continue). CLR and genetic diversity of chromosome 6.
Nature Genetics: doi:10.1038/ng.2312
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Supplementary Figure 2. CLR and genetic diversity of chromosome 2-10 of three maize inbred groups (continue). CLR and genetic diversity of chromosome 7.
Nature Genetics: doi:10.1038/ng.2312
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Supplementary Figure 2. CLR and genetic diversity of chromosome 2-10 of three maize inbred groups (continue). CLR and genetic diversity of chromosome 8.
Nature Genetics: doi:10.1038/ng.2312
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Supplementary Figure 2. CLR and genetic diversity of chromosome 2-10 of three maize inbred groups (continue). CLR and genetic diversity of chromosome 9.
Nature Genetics: doi:10.1038/ng.2312
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Supplementary Figure 2. CLR and genetic diversity of chromosome 2-10 of three maize inbred groups (continue). CLR and genetic diversity of chromosome 10.
Nature Genetics: doi:10.1038/ng.2312
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Supplementary Figure 3. Pedigree of 4 deep sequenced lines.
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Supplementary Figure 4. The length distribution of the 1-10bp indels from 4 deep sequenced inbred lines.
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Supplementary Figure 5. The mutation rate of transition and transversion.
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Supplementary Figure 6. The distribution of allele frequency of SNPs associated with important agronomic traits. These trait-associated SNPs are all from the GWAS studies of NAM population.
Nature Genetics: doi:10.1038/ng.2312
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Supplementary Figure 7. Genetic distance of inbred lines related to B73 and Mo17. A, Genetic distance between six lines (DJ7, LH202, LH149, PB80, LH194 and LH192) and B73. B, Genetic distance between seven lines (LH51, LH54, LH52, LH61, LH57, CR1HT and LH60) and Mo17.
Nature Genetics: doi:10.1038/ng.2312
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Supplementary Figure 8. Distribution of genetic distance of each 5Mb windows. Red line indicates genetic distance of 0.05.
Nature Genetics: doi:10.1038/ng.2312
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References
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