Genotype imputation. (a) Relationship between the accuracy of genotype imputation and the percentage of missing data, which is estimated after removing genotypes over a range of genotype calling probability thresholds. Imputation in Opata (solid lines) and Rialto (dashed lines) cultivars was performed using the reference panel of 60 lines (Opata and Rialto cultivars were excluded) genotyped using the 90 K iSelect assay. (b) Genotype imputation at disease resistance loci. Two GWAS regions overlapped with the positions of the previously mapped Lr37/Yr17/Sr38 (middle panel) and Lr68 (right panel) disease resistance loci; the markers associated with these loci showed highest similarity to CSS contigs 2AS-5264433 and 7BL-6748067, respectively. SNP sites directly genotyped using the 90 K SNP array are shown as red dots; imputed SNPs are shown as black dots.