*2.2. Evaluation of Marker Sets Used in Genomic Prediction*

Four marker sets were used for GP of pasmo resistance. The first marker set contained 52,347 genome-wide SNPs (SNP-52347) that were correlated to the five-year average PS and the PS of the five individual years at a 10−<sup>5</sup> probability level [4]. The other three marker sets were the 500 unique QTL (SNP-500QTL), the 134 QTL statistically stable over five consecutive years (SNP-134QTL) and the 67 stable and relatively large-effect QTL (SNP-67QTL) sets previously identified [4]. The SNP-500QTL dataset comprises markers for all small- or large-effects, including QTL stable across environments and environment-specific QTL identified using three single-locus and seven multi-locus statistical models and all six phenotypic datasets (Figure 2). The SNP-134QTL dataset is a subset of the SNP-500QTL dataset whereas SNP-67QTL is a subset of the former; all SNP-500QTL markers were included in SNP-52347. These four marker sets explained 54%, 72%, 27% and 29% of the phenotypic variation of the five-year PS average (PS-mean), respectively; these values exceeded those of the individual year PS

data (Table 2). Although SNP-500QTL was a subset of SNP-52347, this marker set explained a greater percentage of the phenotypic variation for PS than SNP-52347 for all datasets. *Int. J. Mol. Sci.* **2018**, *19*, x FOR PEER REVIEW 4 of 18

**Figure 1.** Dot plots (lower triangle), histograms (diagonal) and Pearson correlations (upper triangle) between six pasmo severity datasets. Best curves are fitted in dot plots and histograms. \*\*\* represents significance at the <0.001 probability level. **Figure 1.** Dot plots (lower triangle), histograms (diagonal) and Pearson correlations (upper triangle) between six pasmo severity datasets. Best curves are fitted in dot plots and histograms. \*\*\* represents significance at the <0.001 probability level.


PS-2016 0.53 ± 0.06 0.18 ± 0.05 0.18 ± 0.05 0.38 ± 0.07

**Table 2.** Phenotypic variation of pasmo severity (PS) (ℎଶ± *s*) explained by the four marker sets. **Table 2.** Phenotypic variation of pasmo severity (PS) (*h* <sup>2</sup> <sup>±</sup> *<sup>s</sup>*) explained by the four marker sets.

**Figure 2.** Distribution of *R*2 (%) (phenotypic variation explained by individual QTL) in the three QTL marker sets. **Figure 2.** Distribution of *R* 2 (%) (phenotypic variation explained by individual QTL) in the three QTL marker sets.
