Accuracy of genomic prediction using multiple Atlantic salmon populations.

• Published in: Genetics Selection Evolution
• Main Authors: Ajasa, Afees A, Boison, Solomon A, Gjøen, Hans M, Lillehammer, Marie
• Format: Article in Journal/Newspaper
• Language: English
• Published: BioMed Central 2024
• Subjects: Atlantic salmon
• Online Access: https://doi.org/10.1186/s12711-024-00907-5; https://pubmed.ncbi.nlm.nih.gov/38750427

The accuracy of genomic prediction is partly determined by the size of the reference population. In Atlantic salmon breeding programs, four parallel populations often exist, thus offering the opportunity to increase the size of the reference set by combining these populations. By allowing a reduction in the number of records per population, multi-population prediction can potentially reduce cost and welfare issues related to the recording of traits, particularly for diseases. In this study, we evaluated the accuracy of multi- and across-population prediction of breeding values for resistance to amoebic gill disease (AGD) using all single nucleotide polymorphisms (SNPs) on a 55K chip or a selected subset of SNPs based on the signs of allele substitution effect estimates across populations, using both linear and nonlinear genomic prediction (GP) models in Atlantic salmon populations. In addition, we investigated genetic distance, genetic correlation estimated based on genomic relationships, and persistency of linkage disequilibrium (LD) phase across these populations.