Tsuruta S, Misztal I, Lourenco D A L, Lawlor T J
Animal and Dairy Science Department, University of Georgia, Athens 30602.
Animal and Dairy Science Department, University of Georgia, Athens 30602.
J Dairy Sci. 2014 Sep;97(9):5814-21. doi: 10.3168/jds.2013-7821. Epub 2014 Jul 3.
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.
研究了在使用单步基因组最佳线性无偏预测（BLUP）的混合模型方程中分配未知亲本组（UPG），以减少偏差并提高基因组估计育种值（GEBV）的准确性。原始的UPG是根据动物的出生年份和动物未知亲本的性别定义的。重新定义时考虑了将动物出生年份的最后两个UPG合并，以及将美国和非美国荷斯坦牛的UPG分开。使用2011年美国荷斯坦牛最终评分的全国遗传评估中的完整数据集来计算估计育种值（EBV）以进行验证，并使用2011年数据的一个子集（排除2007年之后记录的表型）来计算所有动物的GEBV，包括34500头基因分型公牛。将2007年的EBV和GEBV与2011年完整数据中的EBV进行比较。使用缩减的2007年数据的GEBV模型高估了未知父系和母系的最后一组效应。过去几年中，2011年的EBV和2007年使用原始UPG的GEBV显示出遗传趋势膨胀，而通过合并最后两组重新定义UPG的GEBV则显示出下降。另一方面，通过将美国和非美国荷斯坦牛分开重新定义UPG减少了GEBV中的偏差。2007年没有女儿的年轻基因分型公牛的GEBV对2011年后代偏差的回归系数小于1也表明存在膨胀。UPG的重新定义减少了美国和非美国基因分型公牛的GEBV偏差并略微提高了准确性。2007年和2011年使用重新定义UPG的GEBV之间的秩相关高于没有UPG和原始UPG的情况，特别是对于非美国公牛。在基因组评估中重新定义UPG可以提高GEBV的可靠性并提供正确的遗传趋势。
