%0 Journal Article %1 Tsuruta20145814 %A Tsuruta, S. %A Misztal, I. %A Lourenco, D.A.L. %A Lawlor, T.J. %D 2014 %J Journal of Dairy Science %K 2014 dairy_cattle genomics %N 9 %P 5814 - 5821 %R http://dx.doi.org/10.3168/jds.2013-7821 %T Assigning unknown parent groups to reduce bias in genomic evaluations of final score in \US\ Holsteins %U http://www.sciencedirect.com/science/article/pii/S0022030214004664 %V 97 %X 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.

@article{Tsuruta20145814, abstract = {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. }, added-at = {2016-05-14T05:52:48.000+0200}, author = {Tsuruta, S. and Misztal, I. and Lourenco, D.A.L. and Lawlor, T.J.}, biburl = {https://www.bibsonomy.org/bibtex/2b89ad37b9bdc4734be191cc0b996efae/uga.abgg}, doi = {http://dx.doi.org/10.3168/jds.2013-7821}, interhash = {6cfa9f9267b951df1ba3a00b0c426788}, intrahash = {b89ad37b9bdc4734be191cc0b996efae}, issn = {0022-0302}, journal = {Journal of Dairy Science }, keywords = {2014 dairy_cattle genomics}, number = 9, pages = {5814 - 5821}, timestamp = {2016-05-14T17:49:23.000+0200}, title = {Assigning unknown parent groups to reduce bias in genomic evaluations of final score in \{US\} Holsteins }, url = {http://www.sciencedirect.com/science/article/pii/S0022030214004664}, volume = 97, year = 2014 }