Table 1.
Summary statistics of data sets and corresponding traits.
Figure 1.
Accuracies of WGP in dairy cattle data set.
The solid lines show the change of BLUP|GA accuracy with the overall weight (ω) for fat percentage (red), milk yield (blue), and somatic cell score (green). SNP weights in the BLUP|GA approach were based on the number of QTL reports as described in the ‘Material and Methods’ section. GBLUP corresponds to the scenarios with overall weight ω = 0, and the accuracies of BayesB are presented by horizontal colored dash lines. Accuracies were calculated as the mean of 20 replicates of five-fold cross-validation with variable population size (N = 125, 500 and 2000).
Table 2.
Accuracy and unbiasedness of WGP for dairy cattle.
Figure 2.
Accuracy of WGP for simulated traits with different heritabilities and sample sizes.
The curves show the change of the accuracy obtained with BLUP|GA for varying overall weight ω for milk yield. Different curves represent the accuracies obtained from traits with original phenotype (solid line), or simulated phenotypes with heritability of 0.5 (short-dashed line), 0.3 (point line) and 0.1 (long-dashed line), respectively. The numbers of QTL counts were used to infer the marker weights for the BLUP|GA approach. The GBLUP approach corresponds to scenarios in which ω = 0 (starting points for each curve), and the accuracies of BayesB are presented by horizontal lines. Accuracies were calculated as the mean of 20 replicates of five-fold cross-validation with different population sizes (N = 125, 500, and 2000).
Table 3.
SNP list summary.
Table 4.
Accuracy and unbiasedness of WGP for rice.
Figure 3.
Distribution of reported QTLs positions and marker weights obtained from QTL list.
Reported QTLs associated with fat percentage (red), milk yield (blue) and somatic cell score (green) retrieved from animalQTLdb (http://www.animalgenome.org/animlQTLdb) [17]. Marker weights were calculated as the number of times that each marker was reported to be within a significant QTL region (QTL counts). The colored bar under each plot shows the distribution of QTL positions across the whole genome for the three traits with color keys defined in the first plot (top-right).