Abstract
BackgroundMolecular estimates of breeding value are expected to increase selection response due to improvements in the accuracy of selection and a reduction in generation interval, particularly for traits that are difficult or expensive to record or are measured late in life. Several statistical methods for incorporating molecular data into breeding value estimation have been proposed, however, most studies have utilized simulated data in which the generated linkage disequilibrium may not represent the targeted livestock population. A genomic relationship matrix was developed for 698 Angus steers and 1,707 Angus sires using 41,028 single nucleotide polymorphisms and breeding values were estimated using feed efficiency phenotypes (average daily feed intake, residual feed intake, and average daily gain) recorded on the steers. The number of SNPs needed to accurately estimate a genomic relationship matrix was evaluated in this population.ResultsResults were compared to estimates produced from pedigree-based mixed model analysis of 862 Angus steers with 34,864 identified paternal relatives but no female ancestors. Estimates of additive genetic variance and breeding value accuracies were similar for AFI and RFI using the numerator and genomic relationship matrices despite fewer animals in the genomic analysis. Bootstrap analyses indicated that 2,500-10,000 markers are required for robust estimation of genomic relationship matrices in cattle.ConclusionsThis research shows that breeding values and their accuracies may be estimated for commercially important sires for traits recorded in experimental populations without the need for pedigree data to establish identity by descent between members of the commercial and experimental populations when at least 2,500 SNPs are available for the generation of a genomic relationship matrix.
Highlights
Molecular estimates of breeding value are expected to increase selection response due to improvements in the accuracy of selection and a reduction in generation interval, for traits that are difficult or expensive to record or are measured late in life
The opposite was true for average daily gain (ADG) and rather than reflecting an effect due to sample size, this likely reflects the lack of pedigree information on the dams of these steers which causes them to be treated as unrelated members of the base generation in the analyses that incorporated the numerator relationship matrix (NRM)
The use of the genomic relationship matrix (GRM) corrects for the identity by descent between these dams, which are all derived from a single herd, and should produce higher allele sharing in their sons than would unrelated females
Summary
Molecular estimates of breeding value are expected to increase selection response due to improvements in the accuracy of selection and a reduction in generation interval, for traits that are difficult or expensive to record or are measured late in life. A genomic relationship matrix was developed for 698 Angus steers and 1,707 Angus sires using 41,028 single nucleotide polymorphisms and breeding values were estimated using feed efficiency phenotypes (average daily feed intake, residual feed intake, and average daily gain) recorded on the steers. Phenotypic independence does not guarantee genetic independence between RFI and the traits upon which it has been conditioned [7] and undesirable correlated responses can occur if producers fail to select on appropriate indexes. Because AFI can relatively be assigned an economic value, unlike RFI [8], it is the most logical input trait to include in a selection index [9] which includes economically relevant output traits, to produce the optimal selection tool [10]
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