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Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 509425
Title Combining GWAS and Genomic Prediction using Sequence Information on 5000 Holstein Bulls, effect on Prediction Accuracy
Author(s) Veerkamp, R.F.; Bouwman, A.C.
Event Plant and Animal Genome XXIV Conference, San Diego, 2016-01-09/2016-01-13
Department(s) LR - Animal Breeding & Genomics
Animal Breeding and Genetics
Publication type Abstract in scientific journal or proceedings
Publication year 2016
Abstract Our earlier works (van Binsbergen et al, 2015) showed that using whole genome sequence information did not improve the accuracy for genomic prediction within the Holstein population. In this study we therefore compared genomic prediction using selected SNP from single SNP GWAS with imputed whole genome information (from run4 of the 1000 bull genomes project) to genomic prediction obtained using either the full sequence, 50k or BovineHD SNP chips. The GWAS used highly accurate deregressed proofs from 3416 training bulls, all progeny tested bulls for protein yield, interval first to last insemination and SCC . The analyses were performed in the GCTA package. The genomic relationship matrix was included to account for population structure and was based on the SNP of the bovine HD chip. After the GWAS, the relevance of different selected SNP sets were tested by estimating the h2 and the prediction accuracy in 2287 validation animals, using the GRM calculated with different SNP subsets. From the 30 million SNP in the sequence information, only 13,789,029 where segregating in the Holstein population. For protein yield 2,194 SNPs were significant (-log10(p) >5), and 28 (160) of those were present on the 50k (HD) SNP chips. Within the Holstein population prediction accuracy as well as the h2 were lower when SNPs were selected based on the GWAS, and there was no advantage in comparison with the 50K or BovineHD SNPchips. But more selective selection procedures and training population might be required to benefit from the precision of full sequence genotypes.
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