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Long-term impacts of genome-enabled selection.

Nanye Long1, Daniel Gianola, Guilherme J M Rosa

  • 1Department of Animal Sciences, University of Wisconsin-Madison, WI 53706, USA. nlong@wisc.edu

Journal of Applied Genetics
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Summary

Directional selection using genomic breeding values (GEBVs) decreases prediction accuracy over generations. Higher marker density improves long-term selection response magnitude and duration for quantitative traits.

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Area of Science:

  • Quantitative genetics
  • Genomic selection
  • Animal breeding

Background:

  • Genomic breeding values (GEBVs) are crucial for selecting quantitative traits.
  • Selection impacts GEBV prediction accuracy and genetic architecture.
  • Understanding long-term effects of marker density on selection is needed.

Purpose of the Study:

  • To evaluate directional selection effects on GEBV accuracy and genetic architecture.
  • To assess the influence of marker density on long-term selection response.

Main Methods:

  • Simulations were used to model selection over generations.
  • Bayesian Lasso estimated single-nucleotide polymorphism (SNP) marker effects.
  • GEBVs were calculated using estimated marker effects.

Main Results:

  • GEBV accuracy decreased with selection generations, lower than random selection.
  • Selection response plateaued long-term, but higher marker density increased response.
  • Selection altered quantitative trait loci (QTL) allele frequencies and linkage disequilibrium (LD).

Conclusions:

  • Directional selection reduces GEBV accuracy over time.
  • Higher marker density enhances long-term selection response.
  • Family effects are important for early GEBV accuracy.