Table 6 Average R-squareda (SD) of partitioned verses standard RR-BLUP model for different cross-validation (Table 3), models (Table 4) and effects used to generate the GV and GEBV
R-Squared (SD)
CV40CV20CV10
ComparisonPhenotypic ModelLine Effects to Generate GVbStandard ModelPartitioned ModelMarkerc Effects to Generate GEBVStandard ModelPartitioned ModelStandard ModelPartitioned ModelStandard ModelPartitioned Model
1EDIAG2010SDIAGPDIAG20100.366(0.047)0.406(0.048)0.390(0.055)0.438(0.064)0.404(0.085)0.461(0.093)
2EDIAG2010SDIAGPDIAG20110.333(0.055)0.359(0.062)0.362(0.091)0.383(0.095)0.387(0.139)0.407(0.137)
3EDIAG2011SDIAGPDIAG20110.280(0.043)0.298(0.046)0.304(0.081)0.318(0.081)0.323(0.144)0.334(0.138)
4EDIAG2011SDIAGPDIAG20100.252(0.050)0.288(0.043)0.267(0.070)0.307(0.060)0.277(0.122)0.319(0.097)
5ECS+DIAGTotal 2010SCS+DIAGPCS+DIAGTotal 20100.368(0.044)0.410(0.046)0.392(0.049)0.439(0.061)0.406(0.078)0.462(0.088)
6ECS+DIAGTotal 2011SCS+DIAGPCS+DIAGTotal 20110.360(0.041)0.401(0.043)0.382(0.053)0.428(0.062)0.395(0.089)0.448(0.098)
7EFAM1Total 2010SFAM1PFAM1Total 20100.320(0.044)0.376(0.051)0.335(0.059)0.403(0.071)0.344(0.093)0.423(0.097)
8EFAM1Total 2011SFAM1PFAM1Total 20110.365(0.043)0.402(0.048)0.386(0.052)0.430(0.056)0.396(0.085)0.448(0.083)
9EDIAG2010SCS+DIAGPCS+DIAGMain0.350(0.048)0.392(0.056)0.371(0.068)0.419(0.082)0.387(0.101)0.442(0.115)
10EDIAG2011SCS+DIAGPCS+DIAGMain0.271(0.040)0.302(0.040)0.289(0.066)0.322(0.068)0.300(0.117)0.336(0.115)
11EDIAG2010SFAM1PFAM1Main0.323(0.059)0.377(0.063)0.336(0.087)0.404(0.092)0.349(0.122)0.430(0.125)
12EDIAG2011SFAM1PFAM1Main0.268(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.