Integration of foreign estimates of SNP effects into a domestic SNPBLUP
The aim of this research was to develop and to test different procedures that integrate estimates of single nucleotide polymorphism (SNP) effects and associated measures of precision from a foreign SNP Best Linear Unbiased Prediction (SNPBLUP), into a domestic SNPBLUP when exchange of genotypes or phenotypes is prohibited for whatever reason. In addition to the foreign estimates of SNP effects, procedures were developed assuming the availability of associated: 1) prediction error (co)variance (PEC) matrix; 2) PEC matrix separately for each chromosome; 3) prediction error variances (PEV) only; 4) PEV, allele frequencies, and linkage disequilibrium (LD) of foreign training set; and 5) as 4) but with LD measured on foreign selection candidates. We tested these approaches with a simulation of two historically related populations for a single trait. We confirmed that integrating foreign estimates of SNP effects and the associated PEC matrix led to the same direct genomic values for selection candidates as the joint SNPBLUP using datasets from both populations. Integrating foreign estimates and PEV only led to biased and inaccurate predictions. Procedures based on partial PEC matrices or on LD information gave almost as accurate and unbiased predictions as the joint SNPBLUP. Therefore, accurate integration of foreign estimates of SNP effects into a domestic SNPBLUP seems possible, even if only PEV and some population statistics are available.
- 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).