Table 4 Experiment 2 (296 maize lines), estimated broad-sense heritability and estimated average predictive ability between observed and predicted values for grain yield under drought stress and grain yield under well-watered conditions for 14 models
Trait–Environment
Average Predictive Correlation of GY-SSAverage Predictive
Correlation of GY-WW
Model
 RKHS0.438 (0.093)0.616 (0.059)
 RKHSIM0.442 (0.093)0.616 (0.059)
 RKHSIMS0.454 (0.093)0.606 (0.060)
 RKHSIML0.454 (0.093)0.606 (0.060)
 RKHSH0.417 (0.087)0.543 (0.060)
 RKHSHS0.449 (0.070)0.595 (0.060)
 RKHSHL0.443 (0.094)0.609 (0.057)
 GBLUP0.373 (0.103)0.590 (0.071)
 GBLUPIM0.367 (0.107)0.606 (0.070)
 GBLUPIMS0.385 (0.100)0.612 (0.070)
 GBLUPIML0.385 (0.100)0.612 (0.070)
 GBLUPH0.377 (0.088)0.534 (0.064)
 GBLUPHS0.385 (0.100)0.602 (0.070)
 GBLUPHL0.380 (0.100)0.608 (0.065)
Estimated broad-sense heritability0.3800.441
  • SE shown in parentheses. Average correlations are across 50 random partitions of the data with 70% in the training set and 30% in the validation set. Fitted models were reproducing kernel Hilbert spaces regression without imputed GBS (RKHS), reproducing kernel Hilbert spaces regression with imputed GBS (RKHSIM), reproducing kernel Hilbert spaces regression with haplotype inference form imputed GBS (RKHSH), reproducing kernel Hilbert spaces regression with imputed GBS for short haplotypes (RKHSIMS), reproducing kernel Hilbert spaces regression with haplotype inference from imputed GBS with short haplotypes (RKHSHS), reproducing kernel Hilbert spaces regression with GBS imputation from long haplotypes (RKHSIML), reproducing kernel Hilbert spaces regression with haplotype inference from imputed GBS with long haplotypes (RKHSHL), GBLUP without imputed GBS, GBLUP with imputed GBS (GBLUPIM), GBLUP with haplotype inference from imputed GBS (GBLUPH), GBLUP with imputed GBS from short haplotypes (GBLUPIMS), GBLUP with haplotype inference from imputed GBS with short haplotypes (GBLUPHS), GBLUP with GBS imputation from long haplotypes (GBLUPIML), and GBLUP with haplotype inference from imputed GBS with long haplotypes (GBLUPHL). GBLUP, genomic best linear unbiased predictors; GBS, genotyping-by-sequencing; GY-SS, grain yield under drought stress conditions; GY-WW, grain yield under well-watered conditions.