%0 Journal Article %1 Lourenco20141742 %A Lourenco, D.A.L. %A Misztal, I. %A Tsuruta, S. %A Aguilar, I. %A Ezra, E. %A Ron, M. %A Shirak, A. %A Weller, J.I. %D 2014 %J Journal of Dairy Science %K 2014 dairy_cattle genomics %N 3 %P 1742 - 1752 %R http://dx.doi.org/10.3168/jds.2013-6916 %T Methods for genomic evaluation of a relatively small genotyped dairy population and effect of genotyped cow information in multiparity analyses %U http://www.sciencedirect.com/science/article/pii/S0022030214000526 %V 97 %X Abstract Methods for genomic prediction were evaluated for an Israeli Holstein dairy population of 713,686 cows and 1,305 progeny-tested bulls with genotypes. Inclusion of genotypes of 343 elite cows in an evaluation method that considers pedigree, phenotypes, and genotypes simultaneously was also evaluated. Two data sets were available: a complete data set with production records from 1985 through 2011, and a reduced data set with records after 2006 deleted. For each production trait, a multitrait animal model was used to compute traditional genetic evaluations for parities 1 through 3 as separate traits. Evaluations were calculated for the reduced and complete data sets. The evaluations from the reduced data set were used to calculate parent average for validation bulls, which was the benchmark for comparing gain in predictive ability from genomics. Genomic predictions for bulls in 2006 were calculated using a Bayesian regression method (BayesC), genomic \BLUP\ (GBLUP), single-step \GBLUP\ (ssGBLUP), and weighted ssGBLUP (WssGBLUP). Predictions using BayesC and \GBLUP\ were calculated either with or without an index that included parent average. Genomic predictions that included elite cow genotypes were calculated using ssGBLUP and WssGBLUP. Predictive ability was assessed by coefficients of determination (R2) and regressions of predictions of 135 validation bulls with no daughters in 2006 on deregressed evaluations of those bulls in 2011. A reduction in \R2\ and regression coefficients was observed from parities 1 through 3. Fat and protein yields had the lowest \R2\ for all the methods. On average, \R2\ was lowest for parent averages, followed by GBLUP, BayesC, ssGBLUP, and WssGBLUP. For some traits, \R2\ for direct genomic values from BayesC and \GBLUP\ were lower than those for parent averages. Genomic estimated breeding values using ssGBLUP were the least biased, and this method appears to be a suitable tool for genomic evaluation of a small genotyped population, as it automatically accounts for parental index, allows for inclusion of female genomic information without preadjustments in evaluations, and uses the same model as in traditional evaluations. Weighted ssGBLUP has the potential for higher evaluation accuracy.

@article{Lourenco20141742, abstract = {Abstract Methods for genomic prediction were evaluated for an Israeli Holstein dairy population of 713,686 cows and 1,305 progeny-tested bulls with genotypes. Inclusion of genotypes of 343 elite cows in an evaluation method that considers pedigree, phenotypes, and genotypes simultaneously was also evaluated. Two data sets were available: a complete data set with production records from 1985 through 2011, and a reduced data set with records after 2006 deleted. For each production trait, a multitrait animal model was used to compute traditional genetic evaluations for parities 1 through 3 as separate traits. Evaluations were calculated for the reduced and complete data sets. The evaluations from the reduced data set were used to calculate parent average for validation bulls, which was the benchmark for comparing gain in predictive ability from genomics. Genomic predictions for bulls in 2006 were calculated using a Bayesian regression method (BayesC), genomic \{BLUP\} (GBLUP), single-step \{GBLUP\} (ssGBLUP), and weighted ssGBLUP (WssGBLUP). Predictions using BayesC and \{GBLUP\} were calculated either with or without an index that included parent average. Genomic predictions that included elite cow genotypes were calculated using ssGBLUP and WssGBLUP. Predictive ability was assessed by coefficients of determination (R2) and regressions of predictions of 135 validation bulls with no daughters in 2006 on deregressed evaluations of those bulls in 2011. A reduction in \{R2\} and regression coefficients was observed from parities 1 through 3. Fat and protein yields had the lowest \{R2\} for all the methods. On average, \{R2\} was lowest for parent averages, followed by GBLUP, BayesC, ssGBLUP, and WssGBLUP. For some traits, \{R2\} for direct genomic values from BayesC and \{GBLUP\} were lower than those for parent averages. Genomic estimated breeding values using ssGBLUP were the least biased, and this method appears to be a suitable tool for genomic evaluation of a small genotyped population, as it automatically accounts for parental index, allows for inclusion of female genomic information without preadjustments in evaluations, and uses the same model as in traditional evaluations. Weighted ssGBLUP has the potential for higher evaluation accuracy. }, added-at = {2016-05-14T05:43:05.000+0200}, author = {Lourenco, D.A.L. and Misztal, I. and Tsuruta, S. and Aguilar, I. and Ezra, E. and Ron, M. and Shirak, A. and Weller, J.I.}, biburl = {https://www.bibsonomy.org/bibtex/2a092a5084d4ac511660aacc653746ab7/uga.abgg}, doi = {http://dx.doi.org/10.3168/jds.2013-6916}, interhash = {e6c52cd971c297d8dbfa1aa1f3f22b07}, intrahash = {a092a5084d4ac511660aacc653746ab7}, issn = {0022-0302}, journal = {Journal of Dairy Science }, keywords = {2014 dairy_cattle genomics}, number = 3, pages = {1742 - 1752}, timestamp = {2016-05-14T17:50:55.000+0200}, title = {Methods for genomic evaluation of a relatively small genotyped dairy population and effect of genotyped cow information in multiparity analyses }, url = {http://www.sciencedirect.com/science/article/pii/S0022030214000526}, volume = 97, year = 2014 }