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Long-distance associations generate erosion of genomic breeding values of candidates for selection

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Abstract

Most validation studies of genomic evaluation observe inflation, i.e. regression coefficients of the later phenotypes on early predictions smaller than one. In this paper, we show that this is due to non-zero contributions of distant QTLs, especially those located in other chromosomes than the SNPs. These effects result from linkage disequilibrium (here measured with r 2) present in the reference data but eroded in the population of candidates. In six French dairy cattle breeds average r 2 is low across chromosomes but a substantial proportion of SNP pairs show r values higher than 0.05. A simulation study based on real genotypes from the Normande breed shows that 5% of the SNP effect's variance is explained by distant QTL with associations not maintained across generations. A real Holstein example illustrates extensive across chromosomes covariances between effects. It is thus recommended to erode SNP effects to compute unbiased genomic values of candidates to selection.
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Dates and versions

hal-03731274 , version 1 (20-07-2022)

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  • HAL Id : hal-03731274 , version 1

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D Boichard, S Fritz, P Croiseau, V Ducrocq, B Cuyabano, et al.. Long-distance associations generate erosion of genomic breeding values of candidates for selection. 12th World Congress on Genetics Applied to Livestock Production, Jul 2022, Rotterdam, Netherlands. ⟨hal-03731274⟩
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