View Full Table | Close Full ViewTable 1.

Phenotypic and marker-based prediction accuracy for 13 traits. Marker-based prediction was based on training population size (NTP) = 288.

 
Trait† rP rAA rAK rRR rBA rBB rBC rGS/rP§
Flour yield 0.831 0.648 0.544 0.762A 0.761A 0.740 0.761 0.917
H2O-SRC 0.607A 0.484B 0.475B 0.577C 0.585AC 0.570CD 0.556D 0.963
Heading date 0.891 0.551 0.431 0.748A 0.750AB 0.724 0.746B 0.842
Height 0.851 0.521 0.467 0.740A 0.746AB 0.719 0.739B 0.877
LA-SRC 0.786 0.626A 0.625A 0.750BC 0.757B 0.754C 0.751BC 0.963
Lodging 0.262A 0.190B 0.186B 0.278AC 0.281AC 0.284C 0.232 1.073
NaCO-SRC 0.726 0.592 0.559 0.658AB 0.680A 0.671B 0.656B 0.937
PHS 0.578 0.465A 0.449A 0.553B 0.554B 0.552B 0.553B 0.958
Protein 0.493 0.377 0.303 0.449AB 0.453A 0.446B 0.450B 0.919
Softness 0.774 0.529A 0.507A 0.664BC 0.670B 0.649C 0.664BC 0.866
Suc-SRC 0.799 0.627 0.568 0.736AB 0.741AC 0.727BD 0.734CD 0.927
Test weight 0.568AB 0.470B 0.455B 0.560AB 0.571A 0.560BC 0.554C 1.005
Grain yield 0.205AB 0.186CD 0.180C 0.199AD 0.223B 0.222B 0.174C 1.088
Mean 0.644 0.482 0.442 0.590 0.598 0.586 0.582 0.949
H2O-SRC, water solvent retention capacity; LA-SRC, lactic acid solvent retention capacity; NaCO-SRC, sodium carbonate solvent retention capacity; PHS, preharvest sprouting; Suc-SRC, sucrose solvent retention capacity.
rAA, prediction accuracy of association analysis; rAK, prediction accuracy of association analysis using kinship; rBA, prediction accuracy of BayesA; rBB, prediction accuracy of BayesB; rBC, prediction accuracy of BayesCπ; rGS, genomic selection prediction accuracy; rP, phenotypic prediction accuracy; rRR, prediction accuracy of ridge regression.
§rGS/rP is the ratio of BayesA (BA) and phenotypic accuracy as BA had the highest mean prediction accuracy.
Within each trait, accuracies that share the same letter were not significantly different for α = 0.01.



View Full Table | Close Full ViewTable 2.

Economic weight indices for index selection.

 
Index
Trait† Yield Balanced Quality
Flour yield 1.1 2.1 4.2
Heading date –1.0 –1.0 –1.0
Height –4.0 –4.0 –4.0
LA-SRC –1.1 –2.1 –4.2
Lodging –20.0 –20.0 –20.0
PHS –5.0 –10.0 –10.0
Protein –0.8 –1.6 –3.2
Softness 1.1 2.1 4.2
Suc-SRC –1.1 –2.1 –4.2
Test weight 15.0 15.0 15.0
Grain yield 50.0 40.0 30.0
LA-SRC, lactic acid solvent retention capacity; PHS, preharvest sprouting; Suc-SRC, sucrose solvent retention capacity.



View Full Table | Close Full ViewTable 3.

Phenotypic and genomic selection (GS) prediction accuracy for net merit using the base and Smith-Hazel indices for each economic weight index.

 
Index rP rGS H§ rP/H rGS/H
Base
Yield 0.16 0.21 0.49 0.32 0.44
Balanced 0.14 0.20 0.45 0.32 0.44
Quality 0.17 0.21 0.44 0.38 0.48
Smith-Hazel
Yield 0.33 0.31 0.45 0.73 0.68
Balanced 0.29 0.28 NS# 0.46 0.62 0.62
Quality 0.23 0.28 0.51 0.45 0.55
Mean 0.22 0.25 0.47 0.47 0.54
rP, phenotypic prediction accuracy.
rGS, genomic selection prediction accuracy.
§Square root of the broad-sense heritability (H) for net merit in validation data.
Accuracy divided by H to adjust for error in the validation data.
#NS, not significant. rGS and rP were not significantly different for α = 0.01.