%0 Journal Article %1 Tsuruta20114198 %A Tsuruta, S. %A Misztal, I. %A Aguilar, I. %A Lawlor, T.J. %D 2011 %J Journal of Dairy Science %K 2011 dairy_cattle genomics %N 8 %P 4198 - 4204 %R http://dx.doi.org/10.3168/jds.2011-4256 %T Multiple-trait genomic evaluation of linear type traits using genomic and phenotypic data in \US\ Holsteins %U http://www.sciencedirect.com/science/article/pii/S0022030211004231 %V 94 %X Currently, the \USDA\ uses a single-trait (ST) model with several intermediate steps to obtain genomic evaluations for \US\ Holsteins. In this study, genomic evaluations for 18 linear type traits were obtained with a multiple-trait (MT) model using a unified single-step procedure. The phenotypic type data on up to 18 traits were available for 4,813,726 Holsteins, and single nucleotide polymorphism markers from the Illumina BovineSNP50 genotyping Beadchip (Illumina Inc., San Diego, CA) were available on 17,293 bulls. Genomic predictions were computed with several genomic relationship matrices (G) that assumed different allele frequencies: equal, base, current, and current scaled. Computations were carried out with \ST\ and \MT\ models. Procedures were compared by coefficients of determination (R2) and regression of 2004 prediction of bulls with no daughters in 2004 on daughter deviations of those bulls in 2009. Predictions for 2004 also included parent averages without the use of genomic information. The \R2\ for parent averages ranged from 10 to 34% for \ST\ models and from 12 to 35% for \MT\ models. The average \R2\ for all G were 34 and 37% for \ST\ and \MT\ models, respectively. All of the regression coefficients were <1.0, indicating that estimated breeding values in 2009 of 1,307 genotyped young bulls’ parents tended to be biased. The average regression coefficients ranged from 0.74 to 0.79 and from 0.75 to 0.80 for \ST\ and \MT\ models, respectively. When the weight for the inverse of the numerator relationship matrix (A−1) for genotyped animals was reduced from 1 to 0.7, \R2\ remained almost identical while the regression coefficients increased by 0.11–0.26 and 0.12–0.23 for \ST\ and \MT\ models, respectively. The \ST\ models required about 5 s per iteration, whereas \MT\ models required 3 (6) min per iteration for the regular (genomic) model. The \MT\ single-step approach is feasible for 18 linear type traits in \US\ Holstein cattle. Accuracy for genomic evaluation increases when switching \ST\ models to \MT\ models. Inflation of genomic evaluations for young bulls could be reduced by choosing a small weight for the A−1 for genotyped bulls.

@article{Tsuruta20114198, abstract = {Currently, the \{USDA\} uses a single-trait (ST) model with several intermediate steps to obtain genomic evaluations for \{US\} Holsteins. In this study, genomic evaluations for 18 linear type traits were obtained with a multiple-trait (MT) model using a unified single-step procedure. The phenotypic type data on up to 18 traits were available for 4,813,726 Holsteins, and single nucleotide polymorphism markers from the Illumina BovineSNP50 genotyping Beadchip (Illumina Inc., San Diego, CA) were available on 17,293 bulls. Genomic predictions were computed with several genomic relationship matrices (G) that assumed different allele frequencies: equal, base, current, and current scaled. Computations were carried out with \{ST\} and \{MT\} models. Procedures were compared by coefficients of determination (R2) and regression of 2004 prediction of bulls with no daughters in 2004 on daughter deviations of those bulls in 2009. Predictions for 2004 also included parent averages without the use of genomic information. The \{R2\} for parent averages ranged from 10 to 34% for \{ST\} models and from 12 to 35% for \{MT\} models. The average \{R2\} for all G were 34 and 37% for \{ST\} and \{MT\} models, respectively. All of the regression coefficients were <1.0, indicating that estimated breeding values in 2009 of 1,307 genotyped young bulls’ parents tended to be biased. The average regression coefficients ranged from 0.74 to 0.79 and from 0.75 to 0.80 for \{ST\} and \{MT\} models, respectively. When the weight for the inverse of the numerator relationship matrix (A−1) for genotyped animals was reduced from 1 to 0.7, \{R2\} remained almost identical while the regression coefficients increased by 0.11–0.26 and 0.12–0.23 for \{ST\} and \{MT\} models, respectively. The \{ST\} models required about 5 s per iteration, whereas \{MT\} models required 3 (6) min per iteration for the regular (genomic) model. The \{MT\} single-step approach is feasible for 18 linear type traits in \{US\} Holstein cattle. Accuracy for genomic evaluation increases when switching \{ST\} models to \{MT\} models. Inflation of genomic evaluations for young bulls could be reduced by choosing a small weight for the A−1 for genotyped bulls. }, added-at = {2016-05-15T21:00:53.000+0200}, author = {Tsuruta, S. and Misztal, I. and Aguilar, I. and Lawlor, T.J.}, biburl = {https://www.bibsonomy.org/bibtex/29f875e224156d6fd16ee09c891213a3e/uga.abgg}, doi = {http://dx.doi.org/10.3168/jds.2011-4256}, interhash = {bcf56308185b3cd10f578567308f5359}, intrahash = {9f875e224156d6fd16ee09c891213a3e}, issn = {0022-0302}, journal = {Journal of Dairy Science }, keywords = {2011 dairy_cattle genomics}, number = 8, pages = {4198 - 4204}, timestamp = {2016-05-15T21:00:53.000+0200}, title = {Multiple-trait genomic evaluation of linear type traits using genomic and phenotypic data in \{US\} Holsteins }, url = {http://www.sciencedirect.com/science/article/pii/S0022030211004231}, volume = 94, year = 2011 }