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Table 3 Input changes in joint linkage mapping QTL modeling affect the values of the chromosome-specific residuals more profoundly than the corresponding predicted phenotypic values

From: Limits on the reproducibility of marker associations with southern leaf blight resistance in the maize nested association mapping population

Model 1 2 3 4 5 6
1 4694 RILs, original BLUPs, 1106 map 0.88 0.91 0.81 0.81 0.77
2 SZ 4354 RILs, original BLUPs, 1106 map 0.85 0.87 0.82 0.79
3 PH PH, SZ 4694 RILs, updated BLUPs, 1106 map 0.82 0.79 0.79
4 PH, SZ PH SZ 4354 RILs, updated BLUPs, 1106 map 0.80 0.77
5 GN, SZ GN GN, PH, SZ GN, PH 4354 RILs, original BLUPs, 7386 map 0.80
6 GN, PH, SZ GN, PH GN, SZ GN PH 4354 RILs, original BLUPs, 7386 map
  1. Upper diagonal shows average correlation of residual outcome for each chromosome for 15 pairwise model comparisons. Lower diagonal shows the input(s) that differed in each pair of model comparison. “GN”, “PH”, and “SZ” denote the different genotype inputs: GN, linkage map (1106- vs. 7386-marker map); PH, phenotype inputs (original vs. updated BLUPs); and SZ, sample size (4354 vs. 4694 RILs), respectively. Diagonal shows the three inputs for each model.