Genome-wide association study of leaf architecture in the maize nested association mapping population

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1 Supplementary information for: Genome-wide association study of leaf architecture in the maize nested association mapping population Feng Tian, 1,11 Peter J. Bradbury, 1,2,11 Patrick J. Brown, 1,3 Hsiaoyi Hung, 4 Qi Sun, 5 Sherry Flint-Garcia, 6,7 Torbert R. Rocheford, 3,8 Michael D. McMullen, 6,7 James B. Holland, 4,9 Edward S. Buckler 1,2,10 1 Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA, 2 U.S. Department of Agriculture (USDA) Agricultural Research Service (USDA-ARS), Ithaca, NY 14853, USA, 3 Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA, 4 Department of Crop Science, North Carolina State University, Raleigh, NC 27695, USA, 5 Computational Biology Service Unit, Cornell University, Ithaca, NY 14853, USA, 6 U.S. Department of Agriculture (USDA) Agricultural Research Service (USDA-ARS), Columbia, MO 65211, USA, 7 Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA, 8 Department of Agronomy, Purdue University, Urbana, IL 61801, USA,, 9 U.S. Department of Agriculture (USDA) Agricultural Research Service (USDA-ARS), Raleigh, NC 27695, USA, 10 Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA, 11 These authors contributed equally to the work. Correspondence should be addressed to E.S.B (esb33@cornell.edu).

2 a b c Supplementary Figure 1: QTL allele effect size distribution for three leaf traits. a, Upper leaf angle. 96% of significant alleles showed less than 2.5 effect. b, Leaf length. 93% of significant alleles showed less than 18mm effect. c, Leaf width, 95% of significant alleles showed less than 3mm effect.

3 Observed leaf width of founders (mm) Observed leaf length of founders (mm) Observed upper leaf angle of founders ( ) a b c R² = Predicted upper leaf angle of founders from NAM QTL ( ) R² = Predicted leaf length of founders from NAM QTL (mm) R² = Predicted leaf width of founders from NAM QTL (mm) Supplementary Figure 2: Predicted phenotypes of NAM founders based on NAM QTL models. a, Upper leaf angle. b, Leaf length. c, Leaf width. All significant allelic effects (P<0.05) are added to the observed B73 phenotype to predict other NAM founders phenotype.

4 Supplementary Figure 3: Overview of GWAS results for leaf length. The red dotted lines represent the joint linkage QTL peaks in the scale of negative log 10 of significance of QTLs. The triangle boxes indicate the associations identified by GWAS in the scale of BPP. The blue upward and green downward triangles indicate the associations showing positive and negative effects relative to B73 allele, respectively. The lower part of plot is the recombination rate along the chromosome expressed in cm/mb.

5 Supplementary Figure 4: Overview of GWAS results for leaf width. The red dotted lines represent the joint linkage QTL peaks in the scale of negative log 10 of significance of QTLs. The triangle boxes indicate the associations identified by GWAS in the scale of BPP. The blue upward and green downward triangles indicate the associations showing positive and negative effects relative to B73 allele, respectively. The lower part of plot is the recombination rate along the chromosome expressed in cm/mb.

6 Frequency Frequency Frequency a GWAS SNPs within QTL support interval Random SNPs within QTL support inteval b BPP>=0.05 BPP>=0.10 BPP>=0.20 BPP>=0.30 BPP>=0.40 BPP>= E E E E E E-04 GWAS SNPs within QTL support interval Random SNPs within QTL support interval c BPP>=0.05 BPP>=0.10 BPP>=0.20 BPP>=0.30 BPP>=0.40 BPP>= E E E E E E-02 GWAS SNPs within QTL support interval Random SNPs within QTL support interval BPP>=0.05 BPP>=0.10 BPP>=0.20 BPP>=0.30 BPP>=0.40 BPP>= E E E E E E-04 Supplementary Figure 5: Overlap between associated SNPs and p<0.05 QTL support region. a, Upper leaf angle. b, Leaf length. c, Leaf width. The proportion of associated SNPs within QTL support regions was calculated under each BPP threshold. The expected proportion by chance was obtained by calculating the proportion of the number of HapMap SNPs within QTL support regions. The value under each BPP threshold is the significance of each test for the overlap between GWAS results and QTL support interval under each BPP threshold.

7 Grain yield relative to normal leaf type 15% 10% lg1 lg2 5% 0% -5% % -15% Plant density/ha Supplementary Figure 6: The yield response of lg1 and lg2 leaf type relative to normal leaf type at three plant densities. Data is from the Table1 of Lambert and Johnson The percentage of grain yield change of lg1 and lg2 leaf type relative to normal leaf type was calculated and re-plotted.

8 Proportion of alleles Effect size (s.d.) Cummulative P Power a 1 b MLM(K) GLM(Q) GLM MLM(QK) MLM(K) GLM(Q) GLM MLM(QK) c Observed P 70% 60% 50% 40% 30% 20% 10% d Genetic effect (s.d.) 0.15 QTL SNP % Allelic effect size (s.d.) 0 lg1 lg2 Supplementary Figure 7: Simulation results for upper leaf angle and the allelic effect size in the scale of the phenotypic standard deviation (s.d.) in association panel (n=282). a, Quantile-quantile plots of type I error (false positive) rate of association tests under different models. b, The statistical power of different models under different effect sizes. c, The significant QTL allelic effect size distribution expressed in the unit of phenotypic s.d. in association panel. d, The average effect size of significant QTL alleles and the identified SNPs by GWAS around lg1 and lg2 expressed in the unit of phenotypic s.d. in association panel. The value next to each bar is the absolute leaf angle effect in degree.

9 Supplementary Table 1 Joint QTL mapping summary and QTL by E interaction for upper leaf angle Joint linkage mapping summary QTL by Environment interaction QTL chr cm SS df MS F p Rsq Support interval(cm) a G_Comp b GxE_Comp c G/GxE d m E E E E E m E E E E E m E E E E+08 m E E E E+08 m E E E E+08 m E E E E E m E E E E+08 m E E E E+08 m E E E E E m E E E E E m E E E E E m E E E E+08 m E E E E+08 m E E E E+08 m E E E E+08 m E E E E+08 m E E E E E m E E E E E m E E E E E m E E E E E m E E E E+08 m E E E E+08 m E E E E+08 m E E E E E m E E E E E m E E E E+08 m E E E E E m E E E E E m E E E E E m E E E E+08 Population 5.2E E E Model 7.3E E Error 2.4E E+12 a, P<0.05 support interval for each QTL; b, variance component due to QTL; c, variance component due to QTL by environment interaction; d, the ratio of variance component between QTL and QTL by environment interaction.

10 Supplementary Table 2 Joint QTL mapping summary and QTL by E interaction for leaf length Joint linkage mapping summary QTL by Environment interaction QTL chr cm SS df MS F p Rsq Support interval(cm) a G_Comp b GxE_Comp c G/GxE d m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E m E E Population 8.8E E Model 1.5E Error 4.3E a, P<0.05 support interval for each QTL; b, variance component due to QTL; c, variance component due to QTL by environment interaction; d, the ratio of variance component between QTL and QTL by environment interaction.

11 Supplementary Table 3 Joint QTL mapping summary and QTL by E interaction for leaf width Joint linkage mapping summary QTL by Environment interaction QTL chr cm SS df MS F p Rsq Support interval(cm) a G_Comp b GxE_Comp c G/GxE d m E m E m E m E m E m E m E E m E m E m E E m E m E m E m E m E m E m E m E m E m E m E m E m E m E m E m E m E m E m E m E E m E m E E m E m E Population E Model Error a, P<0.05 support interval for each QTL; b, variance component due to QTL; c, variance component due to QTL by environment interaction; d, the ratio of variance component between QTL and QTL by environment interaction.

12 Supplementary Table 4 Associations (BPP>=0.05) identified by GWAS for upper leaf angle SNP/indel AGP position chr BPP cm allele pvalue effect PZE T/C 6.4E PZE /A 1.7E PZE T/C 7.1E PZE A/G 4.3E PZE /AGCGGC 1.3E PZE A/G 7.6E PZE A/G 1.3E PZE G/- 4.0E PZE T/C 2.1E PZE G/A 3.0E PZE C/T 6.8E PZE C/T 2.0E PZE ATT/ E PZE /ATAT 9.1E PZE A/G 4.1E PZE /CA 7.9E PZE A/G 1.7E PZE C/T 9.5E PZE C/T 9.4E PZE A/G 2.7E PZE G/A 7.2E PZE T/G 3.7E PZE G/A 9.8E PZE G/A 9.0E PZE G/C 1.2E PZE /G 8.6E PZE C/T 7.0E PZE G/A 9.1E PZE A/G 2.7E PZE /TGT 1.0E PZE /GGTCCG 1.2E PZE A/G 1.6E PZE A/G 4.4E PZE A/C 2.9E PZE C/A 2.0E PZE T/C 1.9E PZE C/A 5.5E PZE T/C 1.6E PZE A/G 5.0E PZE A/C 2.6E PZE C/G 1.1E PZE G/A 1.8E PZE G/C 9.1E PZE C/G 7.7E PZE A/C 2.0E PZE C/A 6.4E PZE A/T 1.9E PZE A/G 4.0E PZE A/C 3.0E PZE T/C 1.1E PZE A/C 3.3E

13 Supplementary Table 4 Associations (BPP>=0.05) identified by GWAS for upper leaf angle (continued) SNP/indel AGP position chr BPP cm allele pvalue effect PZE G/A 8.2E PZE A/G 1.9E PZE T/G 3.4E PZE T/C 3.5E PZE T/A 2.1E PZE C/A 5.6E PZE C/T 2.5E PZE TG/-- 3.1E PZE G/A 5.9E PZE C/T 5.9E PZE C/T 5.6E PZE /TGG 2.4E PZE A/G 5.6E PZE C/T 4.4E PZE T/C 1.4E PZE T/G 1.3E PZE T/A 8.0E PZE G/A 5.3E PZE AC/-- 5.1E PZE /A 7.3E PZE /ACCGCA 1.7E PZE /TAGAC 1.1E PZE G/A 5.2E PZE G/C 1.8E PZE /T 2.1E PZE T/C 1.2E PZE G/A 1.4E PZE T/C 3.4E PZE G/A 3.8E PZE G/T 2.0E PZE G/A 4.2E PZE T/C 1.6E PZE C/T 1.9E PZE /TTGCT 8.5E PZE G/A 1.1E PZE A/G 5.4E PZE T/G 5.6E PZE T/C 1.5E PZE C/T 4.1E PZE T/G 3.1E PZE A/G 4.7E PZE T/C 6.8E PZE ACC/ E PZE A/C 2.0E PZE C/A 8.7E PZE /A 6.6E PZE T/G 1.4E PZE G/T 2.3E PZE C/T 7.7E PZE C/T 6.3E PZE C/A 7.4E

14 Supplementary Table 4 Associations (BPP>=0.05) identified by GWAS for upper leaf angle (continued) SNP/indel AGP position chr BPP cm allele pvalue effect PZE /GG 9.2E PZE A/G 2.1E PZE A/C 1.3E PZE C/T 3.4E PZE G/A 4.5E PZE G/A 5.4E PZE T/C 2.9E PZE /TGCGC 1.8E PZE G/A 2.5E PZE G/A 1.5E PZE C/A 5.3E PZE C/T 2.7E PZE A/G 1.4E PZE A/G 1.1E PZE C/G 5.5E PZE G/A 3.3E PZE G/A 1.6E PZE C/T 2.6E PZE /G 2.7E PZE T/A 9.6E PZE T/C 6.9E PZE T/C 1.1E PZE A/T 2.7E PZE G/T 2.1E PZE C/G 1.9E PZE C/G 6.7E PZE G/T 1.6E PZE G/A 5.5E PZE A/G 2.8E PZE T/A 3.6E PZE A/G 3.6E PZE G/A 7.0E PZE C/T 4.3E PZE G/A 2.1E PZE ACTG/ E PZE A/G 6.4E PZE A/G 1.0E PZE C/T 2.1E PZE C/T 6.7E PZE /AGTGTGC 8.3E PZE TCCGT/ E PZE C/T 8.1E PZE /CGC 4.7E PZE C/T 5.6E PZE C/T 1.7E PZE A/C 1.7E PZE C/G 1.2E PZE T/A 7.8E PZE T/C 3.4E PZE T/G 1.2E PZE T/C 1.1E

15 Supplementary Table 4 Associations (BPP>=0.05) identified by GWAS for upper leaf angle (Continued) SNP/indel AGP position chr BPP cm allele pvalue effect PZE G/A 7.1E PZE ACC/ E PZE T/C 1.9E PZE C/T 9.1E PZE C/T 2.9E PZE C/T 9.5E PZE A/C 2.8E PZE C/T 1.1E PZE G/A 5.9E PZE A/- 3.2E PZE A/G 1.3E PZE C/A 3.0E PZE A/G 1.1E PZE G/C 1.1E PZE G/A 7.1E PZE T/C 2.5E PZE T/G 8.6E PZE A/T 9.7E PZE G/A 1.8E PZE A/C 3.2E PZE C/T 3.7E PZE T/C 7.8E PZE T/C 6.2E PZE T/A 4.8E PZE G/C 6.8E PZE A/C 4.8E PZE A/T 8.8E PZE A/G 1.4E PZE /A 2.4E PZE T/C 5.5E PZE A/- 3.9E PZE T/C 2.5E PZE T/G 4.6E PZE /GCT 1.9E PZE /CTGCA 1.8E PZE G/A 8.8E PZE T/C 9.6E PZE T/C 1.3E PZE C/T 9.5E PZE C/T 2.6E PZE G/C 4.5E PZE /GCTCACT 5.0E PZE T/C 1.6E PZE A/C 1.1E PZE A/T 1.7E PZE C/A 6.3E PZE G/A 6.5E PZE /TAGGAA 3.1E PZE T/C 4.9E PZE A/G 4.9E

16 Supplementary Table 5 Associations (BPP>=0.05) identified by GWAS for leaf length SNP/indel AGP position chr BPP cm allele pvalue effect PZE A/T 3.3E PZE A/T 4.8E PZE G/C 4.6E PZE AC/-- 6.2E PZE C/T 1.6E PZE G/A 9.0E PZE C/T 4.1E PZE G/A 6.5E PZE T/C 5.1E PZE G/T 3.5E PZE /CTG 7.2E PZE T/C 1.1E PZE T/A 2.6E PZE /CA 4.2E PZE /CAG 4.0E PZE C/T 2.0E PZE G/A 6.7E PZE G/A 1.3E PZE G/T 5.4E PZE C/T 1.9E PZE G/C 4.5E PZE T/G 1.4E PZE /ACGT 3.4E PZE T/C 1.4E PZE C/T 5.0E PZE /A 9.0E PZE T/C 1.1E PZE G/C 6.2E PZE /GTC 6.2E PZE T/C 2.6E PZE G/A 1.1E PZE G/A 1.6E PZE C/T 7.6E PZE /GTACGT 1.9E PZE G/A 1.7E PZE C/T 9.0E PZE A/T 1.2E PZE /AT 1.6E PZE C/T 6.3E PZE C/G 6.7E PZE A/C 1.7E PZE /AGT 8.2E PZE C/T 9.6E PZE C/G 6.5E PZE /G 1.4E PZE C/T 4.1E PZE G/A 9.2E PZE G/T 1.1E PZE G/A 1.4E PZE C/T 2.0E PZE C/A 8.9E

17 Supplementary Table 5 Associations (BPP>=0.05) identified by GWAS for leaf length (Continued) SNP/indel AGP position chr BPP cm allele pvalue effect PZE C/G 5.8E PZE /ATA 9.6E PZE A/C 4.8E PZE A/G 6.3E PZE T/C 7.4E PZE T/C 2.3E PZE A/C 2.5E PZE C/- 9.6E PZE C/T 2.0E PZE C/T 3.1E PZE /TC 6.2E PZE T/C 1.0E PZE /CCG 2.9E PZE C/A 1.2E PZE T/C 5.9E PZE A/G 1.5E PZE G/A 4.7E PZE /TC 4.8E PZE CC/-- 2.0E PZE C/G 9.6E PZE G/T 3.3E PZE G/T 2.0E PZE C/T 1.1E PZE A/G 2.3E PZE C/T 2.0E PZE T/C 1.7E PZE G/T 2.8E PZE G/C 8.2E PZE G/A 8.9E PZE T/G 9.1E PZE /GG 2.1E PZE CA/-- 1.5E PZE /AAT 5.0E PZE G/A 3.8E PZE /GCCCTG 1.4E PZE G/C 6.0E PZE C/T 6.2E PZE C/G 2.2E PZE A/C 2.7E PZE C/T 5.4E PZE A/G 2.9E PZE A/G 3.0E PZE A/G 4.9E PZE T/G 1.2E PZE G/A 2.8E PZE C/G 1.6E PZE C/G 2.8E PZE /ACGAC 7.2E PZE /GCG 1.3E PZE G/C 6.3E PZE G/C 1.6E

18 Supplementary Table 5 Associations (BPP>=0.05) identified by GWAS for leaf length (Continued) SNP/indel AGP position chr BPP cm allele pvalue effect PZE /T 1.1E PZE T/C 1.3E PZE GAC/ E PZE G/A 1.6E PZE /CA 8.2E PZE G/C 1.4E PZE C/T 3.3E PZE /ATTA 9.3E PZE T/C 1.7E PZE CTG/ E PZE GCT/ E PZE T/G 1.8E PZE /TC 1.9E PZE C/T 8.2E PZE T/G 1.3E PZE G/A 1.9E PZE C/T 3.3E PZE A/G 1.3E PZE A/C 6.1E PZE C/T 1.6E PZE G/A 3.0E PZE C/G 1.1E PZE T/C 1.3E PZE G/A 2.6E PZE T/C 3.0E PZE A/G 1.6E PZE T/G 1.9E PZE G/C 2.8E PZE T/C 3.1E PZE G/A 3.1E PZE C/T 9.2E PZE A/G 5.7E PZE T/A 9.0E PZE T/C 3.8E PZE G/C 2.3E PZE A/C 4.5E PZE A/C 5.0E PZE T/G 4.4E PZE C/T 1.2E PZE T/C 6.2E PZE /TGAT 3.1E PZE C/A 1.4E PZE C/T 8.6E PZE C/A 5.1E PZE /CAG 2.2E PZE G/A 8.5E PZE G/A 2.2E PZE G/A 1.0E PZE TG/-- 7.9E PZE G/T 2.5E PZE C/G 5.6E

19 Supplementary Table 5 Associations (BPP>=0.05) identified by GWAS for leaf length (Continued) SNP/indel AGP position chr BPP cm allele pvalue effect PZE G/A 8.6E PZE G/A 5.7E PZE G/C 1.9E PZE G/A 1.0E PZE A/C 6.3E PZE G/A 1.2E PZE CGA/ E PZE C/G 7.5E PZE C/T 5.4E PZE G/A 4.4E PZE /GCTGCA 3.1E PZE G/A 1.5E PZE A/G 1.4E PZE G/C 1.2E PZE C/G 1.2E PZE G/T 1.1E PZE A/G 4.9E PZE C/A 8.4E PZE T/G 5.7E PZE G/T 5.2E PZE G/A 4.7E PZE G/A 1.9E PZE G/A 6.0E PZE G/T 4.3E PZE /ATGG 4.1E PZE G/T 1.6E PZE C/T 2.2E PZE T/G 1.7E PZE C/G 4.0E PZE G/A 4.9E PZE C/G 1.6E PZE G/T 7.6E PZE G/A 8.6E PZE /GCT 7.9E PZE T/C 7.7E PZE A/G 1.7E PZE /CGGCATG 1.7E PZE T/C 2.8E PZE /ACGC 1.3E PZE T/C 1.2E PZE G/A 1.7E PZE T/- 6.4E PZE /AAA 6.5E PZE T/C 2.3E PZE T/C 1.5E PZE A/G 7.2E PZE T/C 1.7E PZE G/A 1.6E PZE C/A 2.9E PZE /GGGCT 7.3E PZE C/G 7.1E

20 Supplementary Table 5 Associations (BPP>=0.05) identified by GWAS for leaf length (Continued) SNP/indel AGP position chr BPP cm allele pvalue effect PZE G/A 9.7E PZE C/T 1.3E PZE A/G 7.7E PZE A/C 1.6E PZE A/G 1.7E PZE G/A 1.3E PZE GCGGCG/ E PZE /TGTAC 3.6E PZE C/A 2.0E PZE C/T 2.6E PZE T/G 6.3E PZE T/C 2.0E PZE G/C 6.2E PZE C/T 4.8E PZE C/A 2.3E PZE T/G 4.1E PZE /CAGCCCG 6.1E PZE /AACG 3.2E PZE G/T 3.1E PZE /G 9.3E PZE G/C 7.8E PZE G/A 5.4E PZE T/C 4.5E PZE A/T 5.2E PZE T/C 2.0E PZE C/T 9.1E PZE /TCT 1.2E PZE C/T 1.7E PZE A/G 1.6E PZE C/T 1.1E PZE G/- 7.2E PZE /TA 1.5E PZE C/A 6.9E PZE C/T 5.7E PZE AAAA/ E PZE T/G 2.3E PZE T/C 2.9E PZE C/T 3.5E PZE /TC 1.3E PZE /CCTTCG 3.6E PZE T/C 1.6E PZE G/C 4.3E PZE C/A 3.6E PZE C/T 4.4E PZE C/T 5.0E

21 Supplementary Table 5 Associations (BPP>=0.05) identified by GWAS for leaf length (Continued) SNP/indel AGP position chr BPP cm allele pvalue effect PZE G/A 4.6E PZE A/C 3.2E PZE C/T 5.6E PZE A/G 2.9E PZE G/A 1.4E PZE /CGTAGAG 2.2E PZE C/T 1.1E PZE A/G 6.4E PZE C/A 1.5E PZE T/C 4.0E PZE C/A 2.7E PZE GGCC/ E PZE T/C 3.9E PZE G/A 1.7E PZE G/C 2.1E PZE G/C 3.6E PZE G/A 8.9E PZE C/T 5.4E PZE G/A 2.1E PZE G/A 3.0E PZE G/A 2.2E PZE A/G 8.1E PZE A/G 8.1E PZE T/C 3.9E PZE /C 4.8E PZE T/C 5.6E PZE G/A 1.9E PZE A/G 6.6E PZE CGTAC/ E PZE A/T 5.2E PZE C/T 1.8E PZE C/G 1.7E PZE A/G 4.0E PZE T/C 7.8E PZE G/T 5.3E PZE /TTCATAT 4.3E PZE GAC/ E PZE T/C 3.6E

22 Supplementary Table 6 Associations (BPP>=0.05) identified by GWAS for leaf width SNP/indel AGP position chr BPP cm allele pvalue effect PZE A/G 7.1E PZE G/A 2.0E PZE A/G 7.2E PZE C/A 1.1E PZE G/A 1.2E PZE /TGC 1.5E PZE G/A 1.6E PZE A/C 2.7E PZE G/T 6.5E PZE A/T 7.2E PZE /TA 7.7E PZE C/T 2.7E PZE /CTTATGC 8.9E PZE T/G 5.9E PZE C/A 2.8E PZE G/C 1.9E PZE G/A 6.6E PZE C/G 4.9E PZE T/C 9.1E PZE A/C 6.1E PZE C/A 2.2E PZE T/C 8.1E PZE G/C 3.7E PZE A/G 8.1E PZE C/T 8.7E PZE G/A 5.9E PZE C/T 6.3E PZE T/A 8.6E PZE G/A 1.3E PZE G/T 1.5E PZE G/A 2.1E PZE C/T 5.2E PZE C/T 3.1E PZE A/C 4.3E PZE T/A 4.1E PZE G/A 1.2E PZE G/C 1.1E PZE A/- 1.5E PZE G/C 2.9E PZE A/T 9.5E PZE T/C 2.8E PZE C/T 2.3E PZE A/G 1.0E PZE G/A 8.1E PZE C/T 3.4E PZE G/A 8.6E PZE T/C 4.8E PZE G/C 3.0E PZE C/T 4.3E PZE G/C 2.8E PZE T/C 2.9E

23 Supplementary Table 6 Associations (BPP>=0.05) identified by GWAS for leaf width (Continued) SNP/indel AGP position chr BPP cm allele pvalue effect PZE /GAC 1.0E PZE C/T 4.9E PZE C/G 2.0E PZE T/C 2.0E PZE C/A 1.8E PZE T/G 1.2E PZE G/C 6.7E PZE T/G 3.7E PZE G/A 6.2E PZE A/G 3.4E PZE C/T 5.0E PZE T/C 7.8E PZE /TG 2.0E PZE C/A 1.7E PZE C/G 1.7E PZE G/C 1.4E PZE G/C 7.5E PZE /ATGAGAA 8.2E PZE A/G 5.5E PZE C/T 1.0E PZE T/C 3.0E PZE A/G 6.8E PZE C/T 1.8E PZE C/T 1.6E PZE G/A 2.0E PZE C/T 5.3E PZE C/G 1.0E PZE T/C 1.1E PZE GTT/ E PZE G/A 4.6E PZE G/A 2.7E PZE C/G 1.4E PZE A/C 1.9E PZE C/T 2.4E PZE C/T 2.6E PZE /CTTTTGC 3.8E PZE A/G 3.1E PZE T/C 8.4E PZE A/G 9.6E PZE G/A 4.4E PZE C/G 7.4E PZE C/T 1.9E PZE A/G 6.5E PZE C/T 1.1E PZE G/- 1.4E PZE A/C 3.1E PZE C/A 8.4E PZE /GGCA 4.6E PZE C/G 3.1E PZE /GCCATG 6.2E PZE G/C 3.0E

24 Supplementary Table 6 Associations (BPP>=0.05) identified by GWAS for leaf width (Continued) SNP/indel AGP position chr BPP cm allele pvalue effect PZE T/G 8.5E PZE /TT 5.0E PZE G/A 2.1E PZE /TG 4.9E PZE G/A 1.8E PZE C/T 6.3E PZE C/G 7.6E PZE G/T 3.6E PZE T/- 7.0E PZE G/A 2.7E PZE /AGCCC 2.2E PZE C/G 8.0E PZE ATGC/ E PZE A/G 5.2E PZE C/T 1.2E PZE C/G 1.3E PZE A/C 8.4E PZE /AA 1.1E PZE C/G 7.8E PZE /CGGCC 1.5E PZE G/T 7.4E PZE G/A 4.0E PZE C/T 1.3E PZE C/G 8.4E PZE A/G 1.7E PZE T/A 1.2E PZE G/A 2.6E PZE G/A 1.5E PZE G/A 7.0E PZE G/T 2.2E PZE C/A 4.1E PZE G/C 1.6E PZE C/G 4.6E PZE T/G 1.6E PZE C/G 1.4E PZE G/A 6.4E PZE A/T 1.4E PZE T/C 2.2E PZE G/A 3.3E PZE C/A 7.5E PZE C/A 7.6E PZE /A 3.0E PZE A/G 2.9E PZE A/G 2.0E PZE G/A 1.7E PZE CCTGGGAG/ E PZE C/A 2.9E PZE A/T 1.4E PZE C/G 1.1E PZE A/G 1.2E PZE C/T 5.4E