Use of a single-step approach for integrating foreign information into national genomic evaluation in Holstein cattle

Guarini, A.R.; Lourenco, D.A.L.; Brito, L.F.; Sargolzaei, M.; Baes, C. F.; Miglior, F.; Tsuruta, S.; Misztal, I.; Schenkel, F.S. (2019). Use of a single-step approach for integrating foreign information into national genomic evaluation in Holstein cattle. Journal of dairy science, 102(9), pp. 8175-8183. Elsevier 10.3168/jds.2018-15819

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The use of multi-trait across-country evaluation (MACE) and the exchange of genomic information among countries allows national breeding programs to combine foreign and national data to increase the size of the training populations and potentially increase accuracy of genomic prediction of breeding values. By including genotyped and nongenotyped animals simultaneously in the evaluation, the single-step genomic BLUP (GBLUP) approach has the potential to deliver more accurate and less biased genomic evaluations. A single-step genomic BLUP approach, which enables integration of data from MACE evaluations, can be used to obtain genomic predictions while avoiding double-counting of information. The objectives of this study were to apply a single-step approach that simultaneously includes domestic and MACE information for genomic evaluation of workability traits in Canadian Holstein cattle, and compare the results obtained with this methodology with those obtained using a multi-step approach (msGBLUP). By including MACE bulls in the training population, msGBLUP led to an increase in reliability of genomic predictions of 4.8 and 15.4% for milking temperament and milking speed, respectively, compared with a traditional evaluation using only pedigree and phenotypic information. Integration of MACE data through a single-step approach (ssGBLUPIM) yielded the highest reliabilities compared with other considered methods. Integration of MACE data also helped reduce bias of genomic predictions. When using ssGBLUPIM, the bias of genomic predictions decreased by half compared with msGBLUP using domestic and MACE information. Therefore, the reliability and bias of genomic predictions for both traits improved substantially when a single-step approach was used for evaluation compared with a multi-step approach. The use of a single-step approach with integration of MACE information provides an alternative to the current method used in Canadian genomic evaluations.

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