Comparison | Phenotypic Model | Line Effects to Generate GV^{b} | Standard Model | Partitioned Model | Marker Effects to Generate GEBV^{c} | Mean Square Error (SD) | |||||
---|---|---|---|---|---|---|---|---|---|---|---|

CV40 | CV20 | CV10 | |||||||||

Standard Model | Partitioned Model | Standard Model | Partitioned Model | Standard Model | Partitioned Model | ||||||

1 | E_{DIAG} | 2010 | S_{DIAG} | P_{DIAG} | 2010 | 8.13(0.74) | 7.86(0.72) | 7.96(1.09) | 7.64(1.09) | 7.85(1.59) | 7.47(1.57) |

2 | E_{DIAG} | 2010 | S_{DIAG} | P_{DIAG} | 2011 | 8.27(0.55) | 8.10(0.54) | 8.04(0.77) | 7.91(0.78) | 7.82(1.05) | 7.70(1.08) |

3 | E_{DIAG} | 2011 | S_{DIAG} | P_{DIAG} | 2011 | 6.85(0.40) | 6.77(0.39) | 6.72(0.60) | 6.65(0.59) | 6.57(0.90) | 6.52(0.89) |

4 | E_{DIAG} | 2011 | S_{DIAG} | P_{DIAG} | 2010 | 7.06(0.51) | 6.89(0.49) | 6.98(0.73) | 6.80(0.71) | 6.92(1.09) | 6.72(1.01) |

5 | E_{CS+DIAG} | Total 2010 | S_{CS+DIAG} | P_{CS+DIAG} | Total 2010 | 8.01(0.75) | 7.74(0.70) | 7.85(1.09) | 7.53(1.04) | 7.73(1.55) | 7.35(1.49) |

6 | E_{CS+DIAG} | Total 2011 | S_{CS+DIAG} | P_{CS+DIAG} | Total 2011 | 7.02(0.57) | 6.79(0.55) | 6.88(0.77) | 6.61(0.75) | 6.75(1.02) | 6.44(1.01) |

7 | E_{FAM1} | Total 2010 | S_{FAM1} | P_{FAM1} | Total 2010 | 9.98(0.87) | 9.55(0.83) | 9.87(1.39) | 9.34(1.34) | 9.80(2.07) | 9.19(1.96) |

8 | E_{FAM1} | Total 2011 | S_{FAM1} | P_{FAM1} | Total 2011 | 7.02(0.62) | 6.81(0.61) | 6.88(0.87) | 6.63(0.83) | 6.79(1.22) | 6.49(1.13) |

9 | E_{DIAG} | 2010 | S_{CS+DIAG} | P_{CS+DIAG} | Main | 8.06(0.63) | 7.79(0.61) | 7.89(0.87) | 7.58(0.88) | 7.75(1.17) | 7.38(1.18) |

10 | E_{DIAG} | 2011 | S_{CS+DIAG} | P_{CS+DIAG} | Main | 6.87(0.42) | 6.73(0.41) | 6.78(0.59) | 6.62(0.60) | 6.69(0.85) | 6.52(0.86) |

11 | E_{DIAG} | 2010 | S_{FAM1} | P_{FAM1} | Main | 8.21(0.55) | 7.88(0.57) | 8.09(0.77) | 7.66(0.85) | 7.94(1.00) | 7.45(1.15) |

12 | E_{DIAG} | 2011 | S_{FAM1} | P_{FAM1} | Main | 6.89(0.40) | 6.74(0.40) | 6.78(0.57) | 6.61(0.59) | 6.66(0.81) | 6.50(0.85) |

GEBV, genomic estimated breeding value; GV, genotypic value; SD=standard deviation.

↵a The mean square error value is from a linear model for the validation set, in which the GEBV is the covariate and the GV the response. The mean square error shown is the average of the mean square error over the different number of iterations (Table 2). Lower mean square error indicates more accurate and precise estimates of GEBV.

↵b GV are calculated using a phenotypic model with all of the lines.

↵c Marker effects from DIAG form are in bold with year of trial shown, and are equivalent to results from a single trial year analysis, marker effects for the MET analyses are in bold and italic, three marker effects are possible: main, interaction 2010, interaction 2011, with the sum of the (main + interaction) marker effects being equivalent of a total marker effect for a particular year.