Reliabilities of genomic estimated breeding values in Danish Jersey

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In order to optimize the use of genomic selection in breeding plans, it is essential to have reliable estimates of the genomic breeding values. This study investigated reliabilities of direct genomic values (DGVs) in the Jersey population estimated by three different methods. The validation methods were (i) fivefold cross-validation and (ii) validation on the most recent 3 years of bulls.
The reliability of DGV was assessed using squared correlations between DGV and deregressed proofs (DRPs). In the recent 3-year validation model, estimated reliabilities were also used to assess the reliabilities of DGV. The data set consisted of 1003 Danish Jersey bulls with conventional estimated breeding values (EBVs) for 14 different traits included in the Nordic selection index.
The bulls were genotyped for Single-nucleotide polymorphism (SNP) markers using the Illumina 54 K chip. A Bayesian method was used to estimate the SNP marker effects. The corrected squared correlations between DGV and DRP were on average across all traits 0.04 higher than the squared correlation between DRP and the pedigree index. This shows that there is a gain in accuracy
due to incorporation of marker information compared with parent index pre-selection only. Averaged across traits, the estimates of reliability of DGVs ranged from 0.20 for validation on the most recent 3 years of bulls and up to 0.42 for expected reliabilities.
Reliabilities from the cross-validation were on average 0.24. For the individual traits, the reliability varied from 0.12 (direct birth) to 0.39 (milk). Bulls whose sires were included in the reference group had an average reliability of 0.25, whereas the bulls whose sires were not included in the reference group had an average reliability that was 0.05 lower.
Original languageEnglish
JournalAnimal
Volume6
Issue5
Pages (from-to)789-796
Number of pages8
ISSN1751-7311
DOIs
Publication statusPublished - May 2012

    Research areas

  • cross-validation, direct genomic value, genomic selection, reliability, composite breed

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