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. 2013 Dec 6;201(4):1227–1239. doi: 10.1111/nph.12621

Table 4.

Performance of genome-wide prediction in 138 Miscanthus sinensis genotypes based on single-nucleotide variant (SNV) markers filtered using liberal criteria (Table 2)

Traita H 2 b rSorg (SD)c AccuSorg (SD)d rMisc (SD)e AccuMisc (SD)f
Phenology
 DOYFS1.9 0.89 0.76 (0.02) 0.81 (0.02) 0.78 (0.01) 0.82 (0.02)
 AvgeSen.9 0.83 0.64 (0.01) 0.71 (0.01) 0.64 (0.01) 0.71 (0.01)
Morphology/biomass
 BaseDiameter.9 0.52 0.27 (0.05) 0.38 (0.06) 0.29 (0.04) 0.40 (0.06)
 DryMatter.9 0.54 0.06 (0.05) 0.09 (0.07) 0.04 (0.06) 0.05 (0.08)
 LeafLength.7 0.65 0.67 (0.01) 0.83 (0.01) 0.66 (0.01) 0.82 (0.01)
 LeafWidth.7 0.64 0.52 (0.02) 0.65 (0.03) 0.56 (0.01) 0.70 (0.02)
 MaxCanopyHeight.9 0.77 0.35 (0.03) 0.40 (0.03) 0.34 (0.02) 0.39 (0.03)
 Moisture.9 0.59 0.70 (0.01) 0.92 (0.01) 0.73 (0.01) 0.95 (0.01)
 StatureCategory.7 0.48 0.39 (0.03) 0.57 (0.04) 0.43 (0.02) 0.62 (0.03)
 StatureLeafAngle.7 0.50 0.46 (0.03) 0.65 (0.05) 0.47 (0.02) 0.66 (0.03)
 StatureStemAngle.7 0.48 0.37 (0.02) 0.53 (0.03) 0.40 (0.02) 0.58 (0.03)
 StemDiameter.9 0.60 0.51 (0.03) 0.66 (0.04) 0.50 (0.02) 0.65 (0.03)
 TallestStem.9 0.88 0.65 (0.01) 0.69 (0.01) 0.63 (0.01) 0.68 (0.02)
 TransectCount.9 0.51 0.17 (0.04) 0.23 (0.06) 0.27 (0.03) 0.39 (0.04)
Cell wall composition
 Cellulose.8 0.79 0.62 (0.02) 0.70 (0.02) 0.61 (0.02) 0.69 (0.02)
 Hemicellulose.8 0.60 0.25 (0.03) 0.32 (0.04) 0.18 (0.04) 0.24 (0.05)
 Lignin.8 0.66 0.43 (0.02) 0.53 (0.03) 0.35 (0.02) 0.43 (0.03)
Average (SD)g 0.64 0.46 (0.20) 0.57 (0.22) 0.46 (0.20) 0.57 (0.23)

All predictive abilities and accuracies are based on 100 random 10-fold cross-validations (i.e. using a training population with N = 124 genotypes).

a

Trait, phenotypic trait as defined in Table 1.

b

H2, broad-sense heritability (see the Materials and Methods section).

c

rSorg (SD), average predictive ability and standard deviation across 100 random 10-fold cross-validations based on 53 174 SNVs obtained from alignments to the Sorghum bicolor genome.

d

AccuSorg (SD), average accuracy of genome-wide prediction and standard deviation across 100 random 10-fold cross-validations based on 53 174 SNVs obtained from alignments to the S. bicolor genome

e

rMisc (SD), average predictive ability and standard deviation across 100 random 10-fold cross-validations based on 121 771 SNVs obtained from alignments to an M. sinensis pseudo-reference.

f

AccuMisc (SD), average accuracy of genome-wide prediction and standard deviation across 100 random 10-fold cross-validations based on 121 771 SNVs obtained from alignments to an M. sinensis pseudo-reference.

g

Average (SD), overall average and standard deviation across traits.