Genomic Selection in Admixed Populations

Abstract Text: Genomic wide evaluation methods are often conducted using purebred populations.  Training and validation are performed using a select set of purebred animals. This approach fails when SNP estimates are used for genomic prediction in other breeds. In this study, we proposed a multi-compartment model where an SNP effect could differ between breeds. A simulation was carried out using a population of two divergent lines (A and B). The proposed method was compared to the pooled data approach based on the accuracy of predicting the true breeding values. The prediction accuracy using the pooled data approach for line A, was 0.57, 0.49 and 0.30 when α was generated from a uniform distribution between [-2, 2], [-4, 4] and α~ [-8, 8] respectively. Using our proposed method, the corresponding accuracies were 0.65, 0.62 and 0.57, respectively. Similar trend was observed for line B.

Keywords:

Genomic selection

Admixed population

SNP