Investigation on the metafounder concept in ssGBLUP based on a simulated cattle population
Single-step genomic best linear unbiased prediction (ssGBLUP) has become a popular tool for genetic evaluations in dairy cattle populations. The use of the metafounder (MF) concept allows better consideration of relationships within and between founder populations and ensures correct matching of pedigree and genomic relationships.
This study investigates the use of the MF concept in a simulated dairy cattle population where the base population consists of two related and inbred founder populations. The objectives are to compare genetic evaluations with and without MF and to investigate different methods of estimating MF parameters (Γ).
Results show that genetic evaluations using MF are less biased and less inflated compared to evaluations using unknown parent groups or not accounting for the different founder populations. However, testing different methods to estimate Γ revealed a tendency to overestimate the relationships within and between the founder populations, leading to an overestimation of pedigree relationships compared to the genomic relationships.
In summary, the MF concept in ssGBLUP is superior in this simulated scenario with two founder populations, but care must be taken when estimating Γ to ensure consistency between pedigree and genomic relationships. In general, these findings highlight the importance of considering relationships within and between founder populations in single-step genetic evaluations.
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).