Improved genomic validation including extra regressions
Genomic predictions (GEBV) are often validated by predicting later deregressed conventional evaluations or daughter yield deviations (dEBV or DYD) from earlier GEBV. Predicting later GEBV from earlier GEBV could be easier for the public to understand and to verify than standard validation and could be applied to single-step models where the GEBV account for genomic preselection but the later dEBV do not. Genomic validations could also predict deregressed GEBV (dGEBV) that include only the new information from the gain in reliability. Changes in genetic trend or rank can also be tested as in validation of conventional EBV by including extra regressions such as on birth year, parent average (PA), or expected future inbreeding (EFI) from the earlier evaluation. The new validation can compute model squared correlations (R2) that ideally should be high, indicating stable evaluations, and predict GEBV difference (final GEBV – earlier GEBV) to give residual R2 that ideally should be low, indicating that changes in evaluations are not a function of other known factors or the earlier GEBV. The new validation methods were applied to U.S. GEBV and for 7 main traits. For most, the regressions on birth year indicated that genetic trend decreased as daughters were added, the regressions on PA were negative, indicating too much blending of PA with direct genomic value, the regressions on EFI were not significant, and regressions on earlier GEBV were > 1.0 when the extra regressions were included. The model R2 ranged from 48 to 79% and the residual R2 ranged from 3 to 18%. These new, more flexible methods give a more complete picture of GEBV properties and how models may be improved to reduce bias and improve prediction accuracy.
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).