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United States Department of Agriculture

Agricultural Research Service


Location: Avian Disease and Oncology Laboratory

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

item Heidaritabar, Marzieh -
item Vereijken, Addie -
item Muir, William -
item Meuwissen, Theo -
item Cheng, Hans
item Megens, Hendrik-Jan -
item Groenen, Martien -
item Bastiaansen, John -

Submitted to: PLoS Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 22, 2014
Publication Date: N/A

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: Selection with genetic marker data is an intense field of study in both animal and plant breeding. The term “genomic selection” (GS) has been used to describe the simultaneous use in selection of up to hundreds of thousands of Single Nucleotide Polymorphisms (SNPs) across the whole genome. Using a 60K SNP chip across the whole genome of three lines of egg-laying chicken, we compared the impact of two selection methods (GS and traditional BLUP selection), by evaluating allele frequency changes after 2 generations of selection. Differences were demonstrated in the effects of selection methods within and between lines. Average allele frequency change values for GBLUP were larger, 0.064, 0.056 and 0.066, compared with BLUP, 0.045, 0.044 and 0.036, for the three lines respectively. Within line, changes in allele frequencies were on average 51% larger with GS than with BLUP selection. Between lines, the genomic regions with the largest changes in allele frequencies showed little overlap. Empirical thresholds for allele frequency changes were determined from gene dropping in the real pedigrees, and differed considerably between GS (between 0.167 and 0.198) and BLUP selection (between 0.105 and 0.126). With BLUP 35 selected regions were identified. With GS, 70 selected regions were identified (empirical P < 0.05) across the 3 lines, with 30 in line B1, 24 in line B2, and 16 in line W. The difference in the number of selected regions, and in the absolute allele frequency changes within these regions, indicate that GS applies much more locally directed selection than pedigree BLUP.

Last Modified: 8/22/2014
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