Accuracy of breeding values of 'unrelated' individuals predicted by dense SNP genotyping

Background

Recent developments in SNP discovery and high throughput genotyping technology have made the use of high-density SNP markers to predict breeding values feasible. This involves estimation of the SNP effects in a training data set, and use of these estimates to evaluate the breeding values of other ''evaluation'' individuals. Simulation studies have shown that these predictions of breeding values can be accurate, when training and evaluation individuals are (closely) related. However, many general applications of genomic selection require the prediction of breeding values of ''unrelated'' individuals, i.e. individuals from the same population, but not particularly closely related to the training individuals.

Methods

Accuracy of selection was investigated by computer simulation of small populations. Using scaling arguments, the results were extended to different populations, training data sets and genome sizes, and different trait heritabilities.

Results

Prediction of breeding values of unrelated individuals required a substantially higher marker density and number of training records than when prediction individuals were offspring of training individuals. However, when the number of records was 2*N_e*L and the number of markers was 10*N_e*L, the breeding values of unrelated individuals could be predicted with accuracies of 0.88 – 0.93, where N_e is the effective population size and L the genome size in Morgan. Reducing this requirement to 1*N_e*L individuals, reduced prediction accuracies to 0.73–0.83.

Conclusion

For livestock populations, 1N_eL requires about ~30,000 training records, but this may be reduced if training and evaluation animals are related. A prediction equation is presented, that predicts accuracy when training and evaluation individuals are related. For humans, 1N_eL requires ~350,000 individuals, which means that human disease risk prediction is possible only for diseases that are determined by a limited number of genes. Otherwise, genotyping and phenotypic recording need to become very common in the future.