Accuracy of predicting genomic breeding values for residual feed intake in Angus and Charolais beef cattle.

In beef cattle, phenotypic data that are difficult and/or costly to measure, such as feed effi-ciency, and DNA marker genotypes are usually avail-able on a small number of animals of different breeds or populations. To achieve a maximal accuracy of genomic prediction using the phenotype and genotype data, strategies for forming a training population to predict genomic breeding values (GEBV) of the selec-tion candidates need to be evaluated. In this study, we examined the accuracy of predicting GEBV for residual feed intake (RFI) based on 522 Angus and 395 Charo-lais steers genotyped on SNP with the Illumina Bovine SNP50 Beadchip for 3 training population forming strategies: within breed, across breed, and by pooling data from the 2 breeds (i.e., combined). Two other sce-narios with the training and validation data split by birth year and by sire family within a breed were also inves-tigated to assess the impact of genetic relationships on the accuracy of genomic prediction. Three statistical methods including the best linear unbiased prediction with the relationship matrix defined based on the pedi-gree (PBLUP), based on the SNP genotypes (GBLUP), and a Bayesian method (BayesB) were used to predict the GEBV. The results showed that the accuracy of the GEBV prediction was the highest when the prediction was within breed and when the validation population had greater genetic relationships with the training pop-ulation, with a maximum of 0.58 for Angus and 0.64 for Charolais. The within-breed prediction accuracies dropped to 0.29 and 0.38, respectively, when the vali-dation populations had a minimal pedigree link with the training population. When the training population of a different breed was used to predict the GEBV of the validation population, that is, across-breed genomic prediction, the accuracies were further reduced to 0.10 to 0.22, depending on the prediction method used. Pool-ing data from the 2 breeds to form the training popula-tion resulted in accuracies increased to 0.31 and 0.43, respectively, for the Angus and Charolais validation populations. The results suggested that the genetic rela-tionship of selection candidates with the training popu-lation has a greater impact on the accuracy of GEBV using the Illumina Bovine SNP50 Beadchip. Pooling data from different breeds to form the training popula-tion will improve the accuracy of across breed genomic prediction for RFI in beef cattle. [ABSTRACT FROM AUTHOR]