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13 March 2018 A comprehensive comparison between single- and two-step GBLUP methods in a simulated beef cattle population
Mario L. Piccoli, Luiz F. Brito, José Braccini, Fernanda V. Brito, Fernando F. Cardoso, Jaime A. Cobuci, Mehdi Sargolzaei, Flávio S. Schenkel
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Abstract

The statistical methods used in the genetic evaluations are a key component of the process and can be best compared by using simulated data. The latter is especially true in grazing beef cattle production systems, where the number of proven bulls with highly reliable estimated breeding values is limited to allow for a trustworthy validation of genomic predictions. Therefore, we simulated data for 4980 beef cattle aiming to compare single-step genomic best linear unbiased prediction (ssGBLUP), which simultaneously incorporates pedigree, phenotypic, and genomic data into genomic evaluations, and two-step GBLUP (tsGBLUP) procedures and genomic estimated breeding values (GEBVs) blending methods. The greatest increases in GEBV accuracies compared with the parents’ average estimated breeding values (EBVPA) were 0.364 and 0.341 for ssGBLUP and tsGBLUP, respectively. Direct genomic value and GEBV accuracies when using ssGBLUP and tsGBLUP procedures were similar, except for the GEBV accuracies using Hayes’ blending method in tsGBLUP. There was no significant or slight bias in genomic predictions from ssGBLUP or tsGBLUP (using VanRaden’s blending method), indicating that these predictions are on the same scale compared with the true breeding values. Overall, genetic evaluations including genomic information resulted in gains in accuracy >100% compared with the EBVPA. In addition, there were no significant differences between the selected animals (10% males and 50% females) by using ssGBLUP or tsGBLUP.

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Mario L. Piccoli, Luiz F. Brito, José Braccini, Fernanda V. Brito, Fernando F. Cardoso, Jaime A. Cobuci, Mehdi Sargolzaei, and Flávio S. Schenkel "A comprehensive comparison between single- and two-step GBLUP methods in a simulated beef cattle population," Canadian Journal of Animal Science 98(3), 565-575, (13 March 2018). https://doi.org/10.1139/cjas-2017-0176
Received: 1 November 2017; Accepted: 22 January 2018; Published: 13 March 2018
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KEYWORDS
accuracy
beef cattle breeding
exactitude
genomic breeding value
genomic data simulation
genomic selection
reproduction de bovins à bœuf
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