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Additional file 2: Table 1 SNP genotyping of 31 F2s and their parental lines with the barley 50 k iSelect SNP Array. G-1 to G-16 are F2s with normal phenotype, and g-1 to g-15 are variagated F2s. Genotypes for called SNPs were converted to the codes of pink “A”, green “B”, yellow “H” and blank “-”. The WT paent Bowman confers the pink ‘A’ genotype, “B” for the mutant BW397, “H” for heterozygous, and missing data as “-”. The flankeding SNPs, JHI-Hv50k-2016-139,629 and JHI-Hv50k-2016-142,540, were highlighted in yellow. Table 2. Primers used for the analysis of HvPTOX alleles.

This is the supplementary material that accompanies the submission Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation (G3-2021-402618). It includes Figures S1 and S2 and Tables S1-S7.

Additional file 1: Figure 1 Phenotypic comparison between Bowman and BW397. The BW397 mutant produces white anthers (A), spike, awns and flag leaf (B). Figure 2 Gene prediction with the genomic sequence of G11.One PPR protein and DNA gyrase were predicated in sense and antisense strand, respectively. Exons were indicated with rectangles, and straight lines for introns. E, exon; I, intron. The gene structures are drawn to scale. Figure 3 The original gel image cropped for Fig. 4band c. Samples were arranged in the following order (from left to right): Bowman, BW397, Lyallpur and GSHO519. The full-length coding region (F2 + R1, shown in Fig. 4b) and the putative promoter (F4 + R2, shown in Fig. 4c) could not be amplified in mutants, but half of the coding sequence at the 3′ was successfully obtained with primers F3 and R1 (Fig. 4b) in all genotypes. A length polymorphism of 35 bp was detected between promoters (F4 + R2) of Bowman and Lyallpur, which was confirmed by sequencing. A genomic region at 2.5 kb upstream of the start codon (F5 and R3, shown in Fig. 4c) were not amplified in mutants, either. The cropped areas were indicated with white dashed rectangles. Figure 4 The original gel image of RT-PCR cropped for Fig. 4d. RT-PCR analysis with 25, 28 and 30 PCR cycles failed to detect the expression of Hvptox in mutants. Actin was used as the internal control. Samples were arranged in the following order (from left to right): Bowman, BW397, Lyallpur and GSHO519. The cropped areas were indicated with white dashed rectangles. Figure 5 Quantitative real-time PCR (qRT-PCR) analysis of Gpa1 alleles.

Figure S1. Correllelogram depicting positive (blue) and negative (red) correlations among whole plant traits. Color scale on right indicates Pearson correlation coefficient r. Figure S2. Correllelogram depicting positive (blue) and negative (red) correlations among wall composition traits determined by NIR. Color scale on right indicates Pearson correlation coefficient r. Figure S3. Boxplots of (a) ANT, (b) IVDMD, and (c) YLD for each population. Bottom and top of each box represent the first and third quartiles. Horizontal line represents the median, whiskers extend to the most extreme data point that is no more than 1.5 times the interquartile range from the box. Table S1. kin-BLUP regression statistics from 20 replicates of 5-fold CV. Table S2. Partial Least Squares regression statistics from 20 replicates of 5-fold CV. Table S3. Sparse Partial Least Squares Regression statistics from 20 replicates of 5-fold CV. Table S4. BayesB Regression statistics from 5-fold CV. Using 5000 iterations and a 1500 iteration burn-in period (see Methods Section). Table S5. Variance components for selected traits after partitioning based on dominant principal components 1â 3. Table S6: ANOVA of factors influencing prediction accuracy. (DOCX 442 kb)