R-Squared (SD) | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|

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

Comparison | Phenotypic Model | Line Effects to Generate GV^{b} | Standard Model | Partitioned Model | Marker^{c} Effects to Generate GEBV | Standard Model | Partitioned Model | Standard Model | Partitioned Model | Standard Model | Partitioned Model |

1 | E_{DIAG} | 2010 | S_{DIAG} | P_{DIAG} | 2010 | 0.366(0.047) | 0.406(0.048) | 0.390(0.055) | 0.438(0.064) | 0.404(0.085) | 0.461(0.093) |

2 | E_{DIAG} | 2010 | S_{DIAG} | P_{DIAG} | 2011 | 0.333(0.055) | 0.359(0.062) | 0.362(0.091) | 0.383(0.095) | 0.387(0.139) | 0.407(0.137) |

3 | E_{DIAG} | 2011 | S_{DIAG} | P_{DIAG} | 2011 | 0.280(0.043) | 0.298(0.046) | 0.304(0.081) | 0.318(0.081) | 0.323(0.144) | 0.334(0.138) |

4 | E_{DIAG} | 2011 | S_{DIAG} | P_{DIAG} | 2010 | 0.252(0.050) | 0.288(0.043) | 0.267(0.070) | 0.307(0.060) | 0.277(0.122) | 0.319(0.097) |

5 | E_{CS+DIAG} | Total 2010 | S_{CS+DIAG} | P_{CS+DIAG} | Total 2010 | 0.368(0.044) | 0.410(0.046) | 0.392(0.049) | 0.439(0.061) | 0.406(0.078) | 0.462(0.088) |

6 | E_{CS+DIAG} | Total 2011 | S_{CS+DIAG} | P_{CS+DIAG} | Total 2011 | 0.360(0.041) | 0.401(0.043) | 0.382(0.053) | 0.428(0.062) | 0.395(0.089) | 0.448(0.098) |

7 | E_{FAM1} | Total 2010 | S_{FAM1} | P_{FAM1} | Total 2010 | 0.320(0.044) | 0.376(0.051) | 0.335(0.059) | 0.403(0.071) | 0.344(0.093) | 0.423(0.097) |

8 | E_{FAM1} | Total 2011 | S_{FAM1} | P_{FAM1} | Total 2011 | 0.365(0.043) | 0.402(0.048) | 0.386(0.052) | 0.430(0.056) | 0.396(0.085) | 0.448(0.083) |

9 | E_{DIAG} | 2010 | S_{CS+DIAG} | P_{CS+DIAG} | Main | 0.350(0.048) | 0.392(0.056) | 0.371(0.068) | 0.419(0.082) | 0.387(0.101) | 0.442(0.115) |

10 | E_{DIAG} | 2011 | S_{CS+DIAG} | P_{CS+DIAG} | Main | 0.271(0.040) | 0.302(0.040) | 0.289(0.066) | 0.322(0.068) | 0.300(0.117) | 0.336(0.115) |

11 | E_{DIAG} | 2010 | S_{FAM1} | P_{FAM1} | Main | 0.323(0.059) | 0.377(0.063) | 0.336(0.087) | 0.404(0.092) | 0.349(0.122) | 0.430(0.125) |

12 | E_{DIAG} | 2011 | S_{FAM1} | P_{FAM1} | Main | 0.268(0.039) | 0.299(0.040) | 0.287(0.070) | 0.323(0.070) | 0.302(0.128) | 0.338(0.118) |

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

↵a The

*R*-squared value is from a linear model for the validation set in which the GEBV is the covariate and the GV the response, the*R*-squared value shown is the average of the*R*-squared value over the different iterations (Table 2). Large*R*-squared values indicate better predictive ability.↵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.