Which individuals to choose to update the reference population? Minimizing the loss of genetic diversity in animal Genomic Selection programs

Genomic selection is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, genomic selection allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study we propose a modification of the reference population composition to mitigate diversity loss. Since the high cost of phenotyping is the limiting factor for genomic selection our findings are of major economic interest. This study aims to answer the following questions: How would decisions on the reference population affect the breeding population? How to best select individuals to update the reference population and balance maximizing genetic gain and minimizing loss of genetic diversity? We investigated three updating strategies for the reference population: random, truncation and optimal contribution strategies. Optimal contribution maximizes genetic merit for a fixed loss of genetic diversity. A French Montbéliarde dairy cattle population with 50K SNP chip genotypes and simulations over ten generations were used to compare these different strategies using milk production as the trait of interest. Candidates were selected to update the reference population. Prediction bias and both genetic merit and diversity were measured. Changes in the reference population composition slightly affected the breeding population. Optimal contribution strategy appeared to be an acceptable compromise to maintain both genetic gain and diversity in the reference and the breeding populations