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Table 4 Accuracy of across-population genomic prediction (SE) for a trait with a heritability of 0.30 or 0.07 when populations have diverged for T (10 or 50) generations: population A (reference) and population B (validation) based on SNP-BLUP or MixP using the different datasets

From: Within- and across-breed genomic prediction using whole-genome sequence and single nucleotide polymorphism panels

Dataset

h2 = 0.30

h2 = 0.07

T = 10

T = 50

T = 10

T = 50

SNP-BLUP

MixP

SNP-BLUP

MixP

SNP-BLUP

MixP

SNP-BLUP

MixP

45 QTL/Morgan

 WGS data

0.396 (0.017)

0.482 (0.023)

0.276 (0.021)

0.360 (0.030)

0.270 (0.018)

0.286 (0.022)

0.171 (0.023)

0.197 (0.029)

 data3000

−0.004 (0.015)

0.008 (0.016)

0.000 (0.022)

0.026 (0.023)

0.015 (0.016)

0.015 (0.017)

−0.003 (0.019)

−0.003 (0.018)

 data2000

0.001 (0.018)

0.001 (0.027)

0.001 (0.017)

−0.002 (0.017)

0.030 (0.018)

0.032 (0.018)

−0.003 (0.017)

−0.017 (0.023)

 data1000

0.020 (0.019)

0.009 (0.019)

−0.023 (0.019)

−0.005 (0.020)

−0.013 (0.015)

−0.017 (0.015)

−0.009 (0.014)

−0.005 (0.015)

 data200

0.001 (0.013)

−0.010 (0.015)

−0.030 (0.021)

−0.012 (0.017)

0.002 (0.021)

−0.001 (0.022)

−0.034 (0.021)

−0.044 (0.026)

132 QTL/Morgan

 WGS data

0.392 (0.021)

0.403 (0.021)

0.238 (0.019)

0.246 (0.019)

0.209 (0.016)

0.211 (0.015)

0.186 (0.018)

0.186 (0.019)

 data3000

0.022 (0.017)

0.025 (0.017)

0.049 (0.023)

0.052 (0.015)

0.005 (0.016)

0.005 (0.017)

−0.018 (0.019)

−0.018 (0.019)

 data2000

0.013 (0.017)

0.021 (0.019)

−0.003 (0.017)

−0.004 (0.017)

−0.026 (0.014)

−0.018 (0.012)

0.001 (0.015)

0.001 (0.015)

 data1000

0.022 (0.017)

0.028 (0.018)

−0.001 (0.017)

−0.002 (0.017)

0.009 (0.017)

0.009 (0.017)

0.017 (0.018)

0.019 (0.017)

 data200

0.005 (0.017)

0.003 (0.015)

−0.022 (0.014)

−0.019 (0.015)

0.002 (0.014)

0.005 (0.017)

−0.005 (0.017)

−0.005 (0.017)

  1. Accuracy of prediction was measured as the correlation between simulated true and predicted genetic value in the validation dataset