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Title: Systematic Differences in the Response of Genetic Variation to Pedigree and Genome Based Selection Methods

item HEIDARITABAR, MARZIEH - Wageningen University
item VEREIJKEN, ADDIE - Hendrix Genetics
item MUIR, WILLIAM - Purdue University
item MEUWISSEN, THEO - Norwegian University Of Life Sciences
item Cheng, Hans
item MEGENS, HENDRIK-JAN - Wageningen University
item GROENEN, MARTIEN - Wageningen University
item BASTIAANSEN, JOHN - Wageningen University

Submitted to: Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/22/2014
Publication Date: 7/30/2014
Publication URL:
Citation: Heidaritabar, M., Vereijken, A., Muir, W.M., Meuwissen, T., Cheng, H.H., Megens, H., Groenen, M.A., Bastiaansen, J.W. 2014. Systematic Differences in the Response of Genetic Variation to Pedigree and Genome Based Selection Methods. Heredity. 55:1-11. Available:

Interpretive Summary: Genomic selection, which is breeding through the use of genetic markers, is widely touted though not proven as being a new and more efficient method to select for superior animals including chicken. In this study, we showed that the response to selection using genomic selection was superior to current state-of-the-art methods. Furthermore, genomic selection can identify the underlying components, which provides knowledge and more informed means for future selections. In short, our results strongly support the implementation of genomic selection in poultry breeding. If incorporated, commercial breeders will be able to make faster progress resulting in healthier and more productive birds for consumers.

Technical Abstract: Genomic selection (GS) is a DNA-based method of selecting for quantitative traits in animal and plant breeding, and offers a potentially superior alternative to traditional breeding methods that rely on pedigree and phenotype information. Using a 60 K SNP chip with markers spaced throughout the entire chicken genome, we compared the impact of GS and traditional BLUP (best linear unbiased prediction) selection methods applied side-by-side in three different lines of egg-laying chickens. Differences were demonstrated between methods, both at the level and genomic distribution of allele frequency changes. In all three lines, the average allele frequency changes were larger with GS, 0.056 0.064 and 0.066, compared with BLUP, 0.044, 0.045 and 0.036 for lines B1, B2 and W1, respectively. With BLUP, 35 selected regions (empirical Po0.05) were identified across the three lines. With GS, 70 selected regions were identified. Empirical thresholds for local allele frequency changes were determined from gene dropping, and differed considerably between GS (0.167–0.198) and BLUP (0.105–0.126). Between lines, the genomic regions with large changes in allele frequencies showed limited overlap. Our results show that GS applies selection pressure much more locally than BLUP, resulting in larger allele frequency changes. With these results, novel insights into the nature of selection on quantitative traits have been gained and important questions regarding the long-term impact of GS are raised. The rapid changes to a part of the genetic architecture, while another part may not be selected, at least in the short term, require careful consideration, especially when selection occurs before phenotypes are observed.