FIGURE 3.

Estimation of the cumulative effect of GWAS detected SNPs by genomic prediction. (A) Cumulative effect of 20–300 top-ranked SNPs detected by the GWAS of Al and proton tolerance. Cumulative effects and prediction accuracies were calculated using 100 times 5-fold cross-validations using coefficients of determination (r²) and root mean squared error (RMSE) as indexes respectively. (B) Difference rate of Al and proton tolerance between actual RRL and predicted RRL. The orange horizontal dashed line indicates the cutoff for unusual phenotype (|Difference rate| ≥ 0.5). Numbers on or under bar plot represent the accessions showing an unusual phenotype (1: Lm-2, 2: Tsu-0, 3: Voeran-1, 4: Bil-7, 5: Bak-2, 6: Dra-2, 7: Fei-0, 8: Bolin-1, 9: Lp2-2, 10: Pna-17, 11: Nermut-1, 12: Bch-4, 13: Jablo-1, 14: Pa-3, 15: Ct-1, 16: Shigu-2, 17: Dra-2, 18: Buckhorn Pass).