Fig. 6
Distributions of cross-validated interoperability between genomic and phenotypic data. Genotyping platforms were genotyping-by-sequencing (GBS) and whole-genome sequencing (WGS, 3-fold coverage), while phenotypes corresponded to the best linear unbiased estimates for yellow rust (YR) scorings computed across large-scale screening or precision experiments, as well as yield breeding values (BV) computed across estimation experiments. Interoperability was estimated as the genomic prediction accuracy using 80% of the integrated data as training and 20% as validation set in 100 cross-validation runs. Total number (N) of samples with phenotypes and polymorphic SNP markers used for cross-validations according to each genotyping platform are portrayed as table on the left side. In case of GBS*, the same training and validation phenotypes used for WGS were considered. For more details on cross-validations, please see Methods. In distributions, diamonds, horizontal and vertical lines correspond to the average, standard deviation and median, respectively. Violin plots were obtained using the vioplot R package (v0.3.7).
