Figure 1.
Figure 1.

Analysis of line crosses. Each circle is the expected mean and standard deviation (SD) for the genomic-estimated breeding values (GEBVs) of the recombinant inbred progeny from one wheat cross. Results are shown for all 179,101 unique crosses between the 599 wheat lines, using the predicted marker effects in environment 1. In the top right of the figure are crosses between parents with high GEBV and complementary alleles, for which high levels of transgressive segregation are expected.

 


Figure 2.
Figure 2.

Performance of the Gaussian model (GAUSS). The figure depicts the effect of the Gaussian scale parameter (θ in Eq. [6]) on the restricted log-likelihood (LL), the training population accuracy (rtrain), and the cross-validation accuracy (rpred) when predicting sets 5 or 6 in environment 1. For set 5 the restricted maximum likelihood solution for θ (θREML) = 0.5, and for set 6 θREML = 0.4. In both cases rtrain approached 1 as θ → 0, but the trends for rpred were different. For set 5 rpred exhibited an interior maximum near θREML, while for set 6 rpred increased monotonically with θ. Because GAUSS is approximately ridge regression (RR) when θ is large, the contrasting behavior in this figure illustrates why GAUSS had higher rpred than RR for set 5 but vice versa for set 6 (see Table 2).