Table 1 Table of genomic prediction accuracies for eight traits in the CNLM (GY, PH, TW and HD) or W-GY (E1, E2, E3, E4) populations with Embedded Image and Embedded Image. k is the number of principal components removed from the marker matrix prior to calculating subgenome covariance matrices. The first 1 to k principal components were included as fixed effects in the model fit for Embedded Image
CNLMkGYPHTWHD
G (2)a00.601b (0.008)c0.559 (0.007)0.515 (0.010)0.664 (0.009)
ABD (4)0.600 (0.008)0.557 (0.008)0.514 (0.011)0.679 (0.007)
G×G (5)0.604 (0.008)0.637 (0.004)0.576 (0.010)0.712 (0.008)
ABD×ABD (7)0.603 (0.008)0.638 (0.005)0.569 (0.011)0.720 (0.006)
G50.600 (0.009)0.558 (0.007)0.514 (0.011)0.663 (0.010)
ABD0.600 (0.009)0.556 (0.008)0.513 (0.011)0.678 (0.008)
G×G0.602 (0.008)0.624 (0.005)0.560 (0.010)0.701 (0.008)
ABD×ABD0.602 (0.007)0.618 (0.005)0.557 (0.010)0.708 (0.006)
W-GYkE1E2E3E4
G00.501 (0.010)0.493 (0.016)0.356 (0.008)0.457 (0.010)
ABD0.492 (0.012)0.481 (0.023)0.346 (0.010)0.449 (0.011)
G×G0.568 (0.010)0.494 (0.017)0.396 (0.013)0.520 (0.010)
ABD×ABD0.549 (0.011)0.484 (0.023)0.393 (0.015)0.509 (0.013)
G50.502 (0.010)0.491 (0.017)0.354 (0.007)0.458 (0.010)
ABD0.495 (0.011)0.475 (0.024)0.345 (0.010)0.453 (0.011)
G×G0.526 (0.010)0.491 (0.017)0.381 (0.007)0.493 (0.011)
ABD×ABD0.520 (0.012)0.475 (0.023)0.373 (0.013)0.486 (0.012)
  • a Equation.

  • b Mean genomic prediction accuracy across ten replicates of five fold cross validation.

  • c Standard deviation of prediction accuracy across ten replicates are shown in parentheses.