Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2007 Dec;177(4):2389-97.
doi: 10.1534/genetics.107.081190.

The impact of genetic relationship information on genome-assisted breeding values

D Habier  1 , R L Fernando, J C M Dekkers
Affiliations

The impact of genetic relationship information on genome-assisted breeding values

D Habier et al. Genetics. 2007 Dec.

Abstract

The success of genomic selection depends on the potential to predict genome-assisted breeding values (GEBVs) with high accuracy over several generations without additional phenotyping after estimating marker effects. Results from both simulations and practical applications have to be evaluated for this potential, which requires linkage disequilibrium (LD) between markers and QTL. This study shows that markers can capture genetic relationships among genotyped animals, thereby affecting accuracies of GEBVs. Strategies to validate the accuracy of GEBVs due to LD are given. Simulations were used to show that accuracies of GEBVs obtained by fixed regression-least squares (FR-LS), random regression-best linear unbiased prediction (RR-BLUP), and Bayes-B are nonzero even without LD. When LD was present, accuracies decrease rapidly in generations after estimation due to the decay of genetic relationships. However, there is a persistent accuracy due to LD, which can be estimated by modeling the decay of genetic relationships and the decay of LD. The impact of genetic relationships was greatest for RR-BLUP. The accuracy of GEBVs can result entirely from genetic relationships captured by markers, and to validate the potential of genomic selection, several generations have to be analyzed to estimate the accuracy due to LD. The method of choice was Bayes-B; FR-LS should be investigated further, whereas RR-BLUP cannot be recommended.

PubMed Disclaimer

Figures

F<sc>igure</sc> 1.—
Figure 1.—
Simulated population.
F<sc>igure</sc> 2.—
Figure 2.—
Accuracies of GEBVs obtained by fixed regression–least squares (FR–LS), random regression–BLUP (RR–BLUP), and Bayes-B using 100 (top), 1000 (center), and 2000 (bottom) LE markers in comparison to the accuracies for trait-pedigree–BLUP (TP–BLUP). Five hundred trait phenotypes in generation 4 were used as the training data for all methods (96 replicates).
F<sc>igure</sc> 3.—
Figure 3.—
Accuracies of GEBVs obtained by fixed regression–least squares (FR–LS), random regression–BLUP (RR–BLUP), Bayes-B1, and Bayes-B2 in lines 1 and 2 in comparison to the accuracies of EBVs obtained by trait-pedigree–BLUP (TP–BLUP) using 1000 individuals in generation 10 each with a trait phenotype and 1000 SNP markers (160 replicates).
See this image and copyright information in PMC

References

    1. Fernando, R. L., 1998. Genetic evaluation and selection using genotypic, phenotypic and pedigree information. Proceedings of the 6th World Congress on Genetics Applied to Livestock Production, Armidale, NSW, Australia, Vol. 26, pp. 329–336.
    1. Karlin, S., 1984. Theoretical aspects of genetic map functions in recombination processes, pp. 209–228 in Human Population Genetics: The Pittsburgh Symposium, edited by A. Chakravarti. Van Nostrand Reinhold, New York.
    1. Kutner, M. H., C. J. Nachtsheim, J. Neter and W. Li, 2005. Applied Linear Statistical Models, Ed. 5. McGraw-Hill, New York.
    1. Legarra, A., C. Robert-Granie, E. Manfredi and J. M. Elsen, 2007. Does genomic selection work in a mice population? Papers and Abstracts from the Workshop on QTL and Marker-Assisted Selection, edited by A. Legarra. March 22–23, 2007, Toulouse, France.
    1. Malécot, G., 1948. Les Mathématiques de l'Hérédité. Masson, Paris.

Publication types

Substances