Accuracy of genomic prediction using imputed whole-genome sequence data in white layers

Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie
Marzieh HeidaritabarJ W M Bastiaansen

Abstract

There is an increasing interest in using whole-genome sequence data in genomic selection breeding programmes. Prediction of breeding values is expected to be more accurate when whole-genome sequence is used, because the causal mutations are assumed to be in the data. We performed genomic prediction for the number of eggs in white layers using imputed whole-genome resequence data including ~4.6 million SNPs. The prediction accuracies based on sequence data were compared with the accuracies from the 60 K SNP panel. Predictions were based on genomic best linear unbiased prediction (GBLUP) as well as a Bayesian variable selection model (BayesC). Moreover, the prediction accuracy from using different types of variants (synonymous, non-synonymous and non-coding SNPs) was evaluated. Genomic prediction using the 60 K SNP panel resulted in a prediction accuracy of 0.74 when GBLUP was applied. With sequence data, there was a small increase (~1%) in prediction accuracy over the 60 K genotypes. With both 60 K SNP panel and sequence data, GBLUP slightly outperformed BayesC in predicting the breeding values. Selection of SNPs more likely to affect the phenotype (i.e. non-synonymous SNPs) did not improve the accuracy of genomic prediction. Th...Continue Reading

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Citations

Jul 1, 2016·Genetics, Selection, Evolution : GSE·Mario P L CalusRoel F Veerkamp
Dec 3, 2016·Genetics, Selection, Evolution : GSE·Roel F VeerkampMario P L Calus
Jul 25, 2019·Genes·Miguel Pérez-Enciso, Laura M Zingaretti
Aug 27, 2017·Genetics, Selection, Evolution : GSE·Natalia S FornerisMiguel Pérez-Enciso
Dec 4, 2016·Genetics·Miguel Pérez-EncisoAndrés Legarra
Jan 18, 2017·Genetics, Selection, Evolution : GSE·Hossein MehrbanNoelia Ibáñez-Escriche
Nov 22, 2018·Genetics, Selection, Evolution : GSE·Qianqian ZhangMario P L Calus
Sep 25, 2017·Genetics, Selection, Evolution : GSE·Irene van den BergMike E Goddard
Aug 6, 2019·Frontiers in Nutrition·Graeme T AttwoodJeanne M E Jacobs
Jul 5, 2017·Genetics, Selection, Evolution : GSE·Melanie HessDorian Garrick
Jun 13, 2018·G3 : Genes - Genomes - Genetics·David KainerCarsten Külheim
Nov 1, 2017·Genetics, Selection, Evolution : GSE·Aniek C BouwmanMario P L Calus
Dec 10, 2020·Journal of Animal Science and Biotechnology·Shaopan YeZhe Zhang
May 14, 2021·BMC Genomics·Johannes GeibelHenner Simianer
Nov 1, 2021·Molecular Ecology·Bilal AshrafJon Slate

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