H.L. Bradford*,1, Y. Masuda†, P.M. VanRaden,* A. Legarra‡, and I. Misztal†
*Animal Genomics and Improvement Laboratory, Agriculture Research Service, USDA, Beltsville, MD 20705-2350
†Department of Animal and Dairy Science, University of Georgia, Athens 30605
‡GenPhySE, INRA, INPT, ENVT, Université de Toulouse, Castanet-Tolosan, France
1Corresponding author: heather.bradford25@uga.edu
2018 J. Dairy Sci. (?)
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The objective was to compare methods of modeling missing pedigree in single-step genomic BLUP. Options for modeling missing pedigree included ignoring the missing pedigree, unknown parent groups (UPG) based on A or H, and metafounders. The assumptions for the distribution of EBV changed with the different models. We simulated data with 0.3 and 0.1 heritabilities for dairy cattle populations that had more missing pedigrees for lesser genetic merit animals. Predictions for the youngest generation and UPG solutions were compared to the true values for validation. For both traits, ssGBLUP with metafounders provided accurate and unbiased predictions for young animals while also appropriately accounting for genetic trend. Accuracy was least and bias was greatest for ssGBLUP with UPG for H indicating this method was not optimal. For the 0.1 heritability, the UPG accuracy (SE) was -0.48 (0.03) suggesting the poor predictions were caused by poor UPG estimates. Problems with UPG estimates were likely caused by the lesser amount of information available for the lesser heritability trait. Hence, UPG needed to be defined differently based on the trait and amount of information. The G and A22 matrices were more similar for metafounders indicating better scaling of the 2 relationship matrices to be more similar and on the same base. More research was needed to investigate accounting for UPG in A22 to better account for missing pedigrees for genotyped animals.
Keywords: genetic group, metafounder, ssGBLUP, unknown parent group