Genomic and pedigree-based genetic parameters for scarcely recorded traits when some animals are genotyped

A - Papers appearing in refereed journals

Veerkamp, R. F., Mulder, H. A., Thompson, R. and Calus, M. P. L. 2011. Genomic and pedigree-based genetic parameters for scarcely recorded traits when some animals are genotyped. Journal of Dairy Science. 94 (8), pp. 4189-4197.

AuthorsVeerkamp, R. F., Mulder, H. A., Thompson, R. and Calus, M. P. L.

Genetic parameters were estimated using relationships between animals that were based either on pedigree, 43,011 single nucleotide polymorphisms, or a combination of these, considering genotyped and non-genotyped animals. The standard error of the estimates and a parametric bootstrapping procedure was used to investigate sampling properties of the estimated variance components. The data set contained milk yield, dry matter intake and body weight for 517 first-lactation heifers with genotypes and phenotypes, and another 112 heifers with phenotypes only. Multivariate models were fitted using the different relationships in ASReml software. Estimates of genetic variance were lower based on genomic relationships than using pedigree relationships. Genetic variances from genomic and pedigree relationships were, however, not directly comparable because they apply to different base populations. Standard errors indicated that using the genomic relationships gave more accurate estimates of heritability but equally accurate estimates of genetic correlation. However, the estimates of standard errors were affected by the differences in scale between the 2 relationship matrices, causing differences in values of the genetic parameters. The bootstrapping results (with genetic parameters at the same level), confirmed that both heritability and genetic correlations were estimated more accurately with genomic relationships in comparison with using the pedigree relationships. Animals without genotype were included in the analysis by merging genomic and pedigree relationships. This allowed all phenotypes to be used, including those from non-genotyped animals. This combination of genomic and pedigree relationships gave the most accurate estimates of genetic variance. When a small data set is available it might be more advantageous for the estimation of genetic parameters to genotype existing animals, rather than collecting more phenotypes.

Keywordsgenomic selection; heritability; genetic correlation; feed intake
Year of Publication2011
JournalJournal of Dairy Science
Journal citation94 (8), pp. 4189-4197
Digital Object Identifier (DOI)
Open accessPublished as bronze (free) open access
FunderEuropean Union
Funder project or codeCentre for Mathematical and Computational Biology (MCB)
RobustMilk project
Application of statistical methods to predictive biology
Publisher's version
Output statusPublished
Publication dates
Online23 Jul 2011
Publication process dates
Accepted29 Mar 2011
Copyright licensePublisher copyright
PublisherElsevier Science Inc

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