Assigning unknown parent groups to reduce bias in genomic evaluations of final score in US Holsteins

Abstract

Assigning unknown parent groups (UPG) in mixed-model equations using single-step genomic BLUP was investigated to reduce bias and to increase accuracy in genomic estimated breeding values (GEBV). The original UPG were defined based on the animal's birth year and the sex of the animal's unknown parents. Combining the last 2 UPG for the animals’ birth years and separating the UPG for US and non-US Holsteins were considered in the redefinition. A full data set in the 2011 national genetic evaluation of final score in US Holsteins was used to calculate estimated breeding values (EBV) for validation, and a subset of the 2011 data, which excluded phenotypes recorded after 2007, was used to calculate GEBV for all animals, including 34,500 genotyped bulls. The EBV and GEBV in 2007 were compared with EBV in the 2011 full data. The last group effects for unknown sires and dams were overestimated with the GEBV model using the reduced 2007 data. The genetic trends from EBV in 2011 and GEBV in 2007 with the original UPG in the last few years demonstrated inflation, whereas GEBV with the redefined UPG by combining the last 2 groups showed deflation. On the other hand, the redefined UPG by separating for US and non-US Holsteins reduced the bias in GEBV. Regression coefficients smaller than unity for GEBV for young genotyped bulls with no daughters in 2007 on progeny deviations in 2011 also indicated inflation. The redefining of UPG reduced bias and slightly increased accuracy in GEBV for both US and non-US genotyped bulls. Rank correlations between GEBV in 2007 and in 2011 with the redefined UPG were higher than those with no UPG and the original UPG, especially for non-US bulls. Redefining of UPG in genomic evaluation could improve reliability of GEBV and provide correct genetic trends.