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Comparison of genomic breeding values based on single or multiple breed reference populations in US Maine-Anjou beef cattle
The efficiency and advantage of predictors that use genomic information have been identified through previous papers which reported accuracy when the training sets comprised individuals from their own purebreds. Several US beef cattle breed associations have been making an effort to take advantage of genomic predictors in their cattle evaluations. The objective of this study was to estimate accuracies of genomic breeding values using Illumina BovineSNP50 genotypes for the three growth traits (birth, yearling and carcass weights) in US Maine-Anjou beef cattle using single or multiple breed training populations. In single breed analyses, only Maine-Anjou animals were used in training. Maine-Anjou animals were clustered into five-groups using K-means clustering for cross validation for the purpose of reducing the relationships between training and test populations. In multiple breed analyses, direct genomic values (DGV) of the growth traits for about 570 Maine-Anjou animals were estimated using phenotype and genotype data that in addition to Maine-Anjou included about 9,500 animals from nine other breeds (AAN, RAN, BRG, SIM, GVH, RDP, BSH, CHA and HER) in the training population. Accuracies of genomic breeding values were calculated as simple correlations between deregressed estimated breeding values (DEBV) used as observation data and DGV. The accuracies of direct genomic values were 0.23 (0.21), 0.38 (0.34) and 0.31 (0.27) for birth, yearling and carcass weight traits when the training sets comprised from single (or multiple) breeds, respectively. These results demonstrate the feasibility of developing DGV for US Maine-Anjou beef cattle. Also, the accuracies of DGV were slightly lower when multiple other unrelated breeds were added to the training population for Main-Anjou animals. In order to strengthen the advantages through a multiple breed training population, further studies to detect common QTL segregating in Maine-Anjou and to find better markers with greater LD across multiple breeds is required.
Keywords:
genomic breeding values, single or multiple breed, US Maine-Anjou beef cattle