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Table 1 Cross-validation results for method fixed regression-least squares at different threshold values

From: A comparison of five methods to predict genomic breeding values of dairy bulls from genome-wide SNP markers

Trait α nSNP MSEP rEBV,MBV bEBV,MBV
ASI 0.1 197.2 (31.6) 1464 (139.2) 0.52 (0.031) 0.49 (0.059)
  0.01 98.2 (7.1) 1235 (62.1) 0.54 (0.043) 0.58 (0.045)
  0.001 33.0 (5.4) 1090 (124.4) 0.53 (0.036) 0.71 (0.048)
  0.0001 15.0 (1.9) 1108 (136.8) 0.50 (0.043) 0.76 (0.084)
PPT 0.1 215.6 (29.3) 0.0214 (0.0023) 0.35 (0.056) 0.32 (0.059)
  0.01 81.6 (5.0) 0.0156 (0.0016) 0.42 (0.059) 0.48 (0.075)
  0.001 30.0 (4.2) 0.0135 (0.0023) 0.43 (0.089) 0.62 (0.155)
  0.0001 15.4 (2.1) 0.0136 (0.0016) 0.39 (0.076) 0.67 (0.173)
  1. Average number of SNP (nSNP) in the model, mean square error (MSEP), correlation (rEBV,MBV) between EBV and MBV, and regression coefficient (bEBV,MBV) of EBV on MBV for different threshold levels (α) in five cross-validation samples of the training data set, standard error in parentheses; ASI: Australian Selection Index; PPT: protein percentage; P-value used to select SNPs in or out of model.