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Inbreeding in genome-wide selection

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Traditional selection methods, such as sib and best linear unbiased prediction (BLUP) selection, which increased genetic gain by increasing accuracy of evaluation have also led to an increased rate of inbreeding per generation (ΔFG). This is not necessarily the case with genome-wide selection, which also increases genetic gain by increasing accuracy. This paper explains why genome-wide selection reduces ΔFG when compared with sib and BLUP selection. Genome-wide selection achieves high accuracies of estimated breeding values through better prediction of the Mendelian sampling term component of breeding values. This increases differentiation between sibs and reduces coselection of sibs and ΔFG. The high accuracy of genome-wide selection is expected to reduce the between family variance and reweigh the emphasis of estimated breeding values of individuals towards the Mendelian sampling term. Moreover, estimation induced intraclass correlations of sibs are expected to be lower in genome-wide selection leading to a further decrease of coselection of sibs when compared with BLUP. Genome-wide prediction of breeding values, therefore, enables increased genetic gain while at the same time reducing ΔFG when compared with sib and BLUP selection.
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Keywords: Genome-wide selection; Mendelian sampling term; inbreeding

Document Type: Research Article

Affiliations: 1:  Sustainable Livestock Systems, Scottish Agriculture College, West Mains Road, Edinburgh, UK 2:  Animal Breeding and Genomics Centre, Wageningen Institute of Animal Sciences, Wageningen University and Research Centre, Wageningen, The Netherlands 3:  Genetics and Genomics, Roslin Institute (Edinburgh), Roslin, Midlothian, UK

Publication date: December 1, 2007

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