Table 3 Experiment 1 (504 doubled-haploid maize lines), estimated broad-sense heritability and average predictive ability between observed and predicted values for grain yield, days to anthesis, and anthesis-silking interval for 13 models and their percent change relative to the pedigree model
ModelGrain YieldDays to AnthesisAnthesis-Silking Interval
Estimated broad-sense heritability0.4330.6760.545
Average predictive correlation
 P0.518 (0.045)0.589 (0.033)0.588 (0.046)
 RKHS0.553 (0.046)0.711 (0.036)0.591 (0.044)
 RKHSIM0.545 (0.045)0.710 (0.035)0.585 (0.044)
 RKHSH0.505 (0.050)0.659 (0.040)0.561 (0.046)
 PRKHS0.584 (0.044)0.727 (0.032)0.620 (0.043)
 PRKHSIM0.582 (0.045)0.729 (0.031)0.616 (0.043)
 PRKHSH0.548 (0.047)0.681 (0.036)0.598 (0.044)
 GBLUP0.469 (0.050)0.668 (0.042)0.563 (0.050)
 GBLUPIM0.475 (0.050)0.677 (0.040)0.566 (0.050)
 GBLUPH0.462 (0.052)0.622 (0.045)0.549 (0.051)
 PGBLUP0.582 (0.045)0.727 (0.031)0.623 (0.042)
 PGBLUPIM0.585 (0.044)0.731 (0.031)0.620 (0.043)
 PGBLUPH0.551 (0.047)0.678 (0.036)0.599 (0.044)
% Change relative to the P model
 RKHS6.720.70.6
 RKHSIM5.220.6−0.6
 RKHSH−2.611.9−4.7
 PRKHS12.723.45.3
 PRKHSIM12.323.84.6
 PRKHSH5.715.61.6
 GBLUP−9.513.4−4.3
 GBLUPIM−8.314.9−3.8
 GBLUPH−10.85.6−6.7
 PGBLUP12.423.45.9
 PGBLUPIM13.024.25.4
 PGBLUPH6.415.11.8
  • 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 pedigree (P), 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 from imputed GBS (RKHSH), GBLUP without imputed GBS, GBLUPSIM with imputed GBS, GBLUPH with haplotype inferred from imputed GBS, pedigree reproducing kernel Hilbert spaces regression without imputed GBS (PRKHS), pedigree reproducing kernel Hilbert spaces regression with imputed GBS (PRKHSIM), pedigree reproducing kernel Hilbert spaces regression with haplotype inference from imputed GBS (PRKHH), pedigree GBLUP without imputed GBS (PGBLUP), pedigree GBLUPSIM with imputed GBS (PGBLUPSIM), and pedigree GBLUPH with haplotype inferred from imputed GBS (PGBLUPH). GBLUP, genomic best linear unbiased predictors; GBS, genotyping-by-sequencing.