Table 2.
Heritability of cross-validated stripe rust prediction models within and across years (2008–2018)
| Year | N | GBLUP | GBLUP-A | GRKHS | GRKHS-A | PBLUP | PBLUP-A | PRKHS | PRKHS-A | Overall |
|---|---|---|---|---|---|---|---|---|---|---|
| 2008 | 47 | 0.70 ± 0.34 b | 0.26 ± 0.39 c | 0.98 ± 0.07 a | 0.77 ± 0.35 b | 0.31 ± 0.35 c | 0.18 ± 0.34 c | 0.15 ± 0.33 c | 0.11 ± 0.31 c | 0.44 ± 0.45 f |
| 2009 | 93 | 0.54 ± 0.19 d | 0.78 ± 0.15 c | 0.86 ± 0.12 b | 0.99 ± 0.04 a | 0.89 ± 0.10 b | 0.92 ± 0.08 ab | 0.86 ± 0.14 b | 0.90 ± 0.12 b | 0.84 ± 0.18 a |
| 2010 | 182 | 0.33 ± 0.09 e | 0.35 ± 0.08 e | 0.63 ± 0.14 cd | 0.68 ± 0.11 bc | 0.76 ± 0.11 a | 0.68 ± 0.15 bc | 0.75 ± 0.14 ab | 0.59 ± 0.16 d | 0.60 ± 0.20 de |
| 2011 | 243 | 0.26 ± 0.12 cd | 0.08 ± 0.05 f | 0.51 ± 0.13 a | 0.31 ± 0.07 bc | 0.32 ± 0.13 b | 0.25 ± 0.08 d | 0.12 ± 0.05 ef | 0.16 ± 0.03 e | 0.26 ± 0.16 h |
| 2012 | 288 | 0.45 ± 0.08 e | 0.39 ± 0.07 f | 0.86 ± 0.07 a | 0.83 ± 0.07 ab | 0.79 ± 0.06 b | 0.68 ± 0.10 c | 0.65 ± 0.07 c | 0.60 ± 0.08 d | 0.66 ± 0.18 bc |
| 2013 | 266 | 0.43 ± 0.08 d | 0.39 ± 0.07 d | 0.87 ± 0.06 a | 0.85 ± 0.06 ab | 0.82 ± 0.11 b | 0.88 ± 0.08 a | 0.58 ± 0.09 c | 0.55 ± 0.08 c | 0.67 ± 0.21 bc |
| 2014 | 1458 | 0.58 ± 0.03 e | 0.31 ± 0.03 g | 0.97 ± 0.01 a | 0.89 ± 0.04 b | 0.49 ± 0.05 f | 0.47 ± 0.06 f | 0.67 ± 0.04 c | 0.62 ± 0.06 d | 0.63 ± 0.21 cd |
| 2015 | 1298 | 0.51 ± 0.04 e | 0.31 ± 0.06 f | 0.97 ± 0.01 a | 0.91 ± 0.03 a | 0.68 ± 0.04 c | 0.61 ± 0.07 d | 0.81 ± 0.14 b | 0.34 ± 0.19 f | 0.64 ± 0.25 cd |
| 2016 | 1387 | 0.43 ± 0.02 d | 0.44 ± 0.03 d | 0.83 ± 0.02 b | 0.83 ± 0.02 b | 0.65 ± 0.02 c | 0.64 ± 0.02 c | 0.86 ± 0.01 a | 0.86 ± 0.01 a | 0.69 ± 0.17 b |
| 2017 | 638 | 0.32 ± 0.06 c | 0.33 ± 0.08 c | 0.69 ± 0.09 a | 0.69 ± 0.10 a | 0.69 ± 0.05 a | 0.69 ± 0.05 a | 0.57 ± 0.15 b | 0.56 ± 0.12 b | 0.57 ± 0.18 e |
| 2018 | 1639 | 0.21 ± 0.04 d | 0.20 ± 0.01 d | 0.54 ± 0.04 a | 0.51 ± 0.03 b | 0.29 ± 0.02 c | 0.29 ± 0.02 c | 0.54 ± 0.03 a | 0.53 ± 0.03 a | 0.39 ± 0.15 g |
| Across | 5233 | 0.34 ± 0.01 f | 0.27 ± 0.01 g | 0.79 ± 0.02 b | 0.73 ± 0.02 c | 0.64 ± 0.02 d | 0.58 ± 0.02 e | 0.86 ± 0.01 a | 0.79 ± 0.02 b | 0.63 ± 0.21 cd |
| Overall | 0.42 ± 0.19 e | 0.34 ± 0.21 f | 0.79 ± 0.17 a | 0.75 ± 0.21 a | 0.61 ± 0.24 bc | 0.57 ± 0.26 cd | 0.62 ± 0.27 b | 0.55 ± 0.27 d |
Each model was five-fold cross-validated with 10 replications within years and across years. Heritability was estimated as the proportion of the total variance explained by the random genotypic term within each fold of each replication. Means ± standard deviations for heritability are displayed. For comparisons among models within each year and overall, groups within each table row that are not connected by the same letter have significantly different heritability (Tukey’s HSD test, p < 0.05). For overall comparisons among years, groups within the last table column that are not connected by the same letter have significantly different heritability (Tukey’s HSD test, p < 0.05). OLS ordinary least squares. GBLUP genomic best linear unbiased prediction. GBLUP-A GBLUP with QTL covariates. GRKHS genomic reproducing kernel Hilbert spaces prediction. GRKHS-A GRKHS with QTL covariates. PBLUP pedigree-based best linear unbiased prediction. PBLUP-A PBLUP with QTL covariates. PRKHS pedigree-based reproducing kernel Hilbert spaces prediction. PRKHS-A PRKHS with QTL covariates
p < 0.05 are italicized