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Figure S3. Manhattan plots for grain yield and related traits in each environment and BLUE value in the diverse panel based on SNP-GWAS. a, grain yield; b, spike number per square meter; c, kernel number per spike; d, thousand-kernel weight; e, kernel length; f, kernel width; g, spike length; h, spike dry weight; i, heading date; j, plant height; k, uppermost internode length; l, flag leaf length; m, flag leaf width; 1, 2012–2013 Anyang; 2, 2012–2013 Suixi; 3, 2013–2014 Anyang; 4, 2013–2014 Suixi; 5, 2014–2015 Anyang; 6, 2014–2015 Shijiazhuang. (DOCX 11525 kb)

Table S1. Analysis of phenotypic data for grain yield and related traits in the diverse panel. (DOCX 16 kb)

Figure S3. Manhattan plots for grain yield and related traits in each environment and BLUE value in the diverse panel based on SNP-GWAS. a, grain yield; b, spike number per square meter; c, kernel number per spike; d, thousand-kernel weight; e, kernel length; f, kernel width; g, spike length; h, spike dry weight; i, heading date; j, plant height; k, uppermost internode length; l, flag leaf length; m, flag leaf width; 1, 2012–2013 Anyang; 2, 2012–2013 Suixi; 3, 2013–2014 Anyang; 4, 2013–2014 Suixi; 5, 2014–2015 Anyang; 6, 2014–2015 Shijiazhuang. (DOCX 11525 kb)

Table S4. Genome coverage, physical distance and marker polymorphism. (DOCX 16 kb)

Table S3. Correlation coefficients among grain yield and related traits in the diverse panel. (DOCX 13 kb)

Figure S4. Manhattan plots for grain yield and related traits in each environment and BLUE value in the diverse panel based on Haplotype-GWAS. See footnote to Fig. S3 for traits and experimental sites. (DOCX 13093 kb)

Table S5. Composition and lengths of blocks and haplotypes. (DOCX 14 kb)

Figure S2. Coverage of SNPs (a) and haplotypes (b) on all 21 bread wheat chromosomes. (DOCX 1094 kb)

Figure S1. Distribution of phenotypic values for grain yield and related traits in the diverse panel. GY, grain yield; SN, spike number per square meter; KNS, kernel number per spike; TKW, thousand-kernel weight; KL, kernel length; KW, kernel width; SL, spike length; SDW, spike dry weight; HD, heading date; PH, plant height; UIL, uppermost internode length; FLL, flag leaf length; FLW, flag leaf width. (DOCX 54 kb)

Table S2. Analysis of variance and broad-sense heritabilities (h2) for grain yield and related traits. (DOCX 13 kb)

Black point scores evaluated for 166 wheat accessions. Reported values are the best linear unbiased predictions (BLUP) value for black point scores across five environments. (DOCX 430Â kb)

Black point scores evaluated for 166 wheat accessions. Reported values are the best linear unbiased predictions (BLUP) value for black point scores across five environments. (DOCX 430Â kb)

Frequency distributions for black point scores for 166 wheat accessions in five environments. (a) Anyang 2013; (b) Anyang 2014; (c) Anyang 2015; (d) Suixi 2013; (e) Suixi 2014; (f) Best linear unbiased predictions (BLUP) value for black point scores across five environments. (DOCX 292Â kb)

The 166 wheat accessions used in the genome-wide association study (GWAS) for black point reaction and their origins. (DOCX 27Â kb)

Basic statistical analysis of SNP markers used for genome-wide association study (GWAS) of 166 wheat accessions. (DOCX 19Â kb)

Basic statistical analysis of SNP markers used for genome-wide association study (GWAS) of 166 wheat accessions. (DOCX 19Â kb)

LD heatmap of all wheat chromosomes showing extent of pairwise linkage disequilibrium between SNP markers significantly associated with black point reactions. (DOCX 4561Â kb)

LD decay estimated in 166 wheat accessions based on 12,324 markers from the 90 K and 660 K SNP arrays. (DOCX 97 kb)

Accessions with high black point resistance. (DOCX 17Â kb)

Quantile-quantile (Q-Q) plot for black point scores in 166 wheat accessions by the mixed linear model (MLM) in Tassel v5.0. (a) Anyang 2013; (b) Anyang 2014; (c) Anyang 2015; (d) Suixi 2013; (e) Suixi 2014; (f) Best linear unbiased predictions (BLUP) value for black point scores across five environments. (DOCX 682Â kb)

LD decay estimated in 166 wheat accessions based on 12,324 markers from the 90 K and 660 K SNP arrays. (DOCX 97 kb)

Quantile-quantile (Q-Q) plot for black point scores in 166 wheat accessions by the FarmCPU. (a) Anyang 2013; (b) Anyang 2014; (c) Anyang 2015; (d) Suixi 2013; (e) Suixi 2014; (f) Best linear unbiased predictions (BLUP) value for black point scores across five environments. (DOCX 379Â kb)