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Practical Considerations When Using Mendelian Sampling Variances for Selection Decisions in Genomic Selection

Tobias A M Niehoff1, Jan Ten Napel1, Mario P L Calus1

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Journal of Animal Breeding and Genetics = Zeitschrift Fur Tierzuchtung Und Zuchtungsbiologie
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PubMed
Summary
This summary is machine-generated.

New selection criteria for livestock breeding consider future genetic variances, maintaining more genetic diversity without sacrificing commercial gain. These methods offer equal or better performance than traditional genomic estimated breeding values (GEBV) in pig breeding simulations.

Keywords:
Mendelian sampling variancebreeding planninggenetic varianceprogeny varianceselection decisionsusefulness criterion

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Area of Science:

  • Animal Breeding and Genetics
  • Quantitative Genetics
  • Genomic Selection

Background:

  • Traditional livestock breeding programs often rely on estimated breeding values (EBVs) or genomic estimated breeding values (GEBV) which may not fully account for long-term genetic diversity.
  • Previous selection criteria in large-scale livestock breeding have not explicitly considered the genetic variances of future generations, especially with estimated marker effects.

Purpose of the Study:

  • To evaluate the application of novel selection criteria that incorporate genetic variances of future generations in large-scale livestock breeding programs.
  • To compare the effectiveness of variance-considering criteria against traditional selection methods using genomic estimated breeding values (GEBV) in a simulated pig breeding program.

Main Methods:

  • A generic pure-line pig breeding program was simulated, selecting 40 males and 400 females annually for daily gain.
  • Three variance-considering selection criteria were compared against standard GEBV selection across various reference population sizes and prediction accuracies.
  • The study analyzed the impact of planning horizon and reference population size on the effectiveness of variance-considering criteria.

Main Results:

  • All variance-considering criteria successfully retained more genetic variance (up to 20% more) compared to selection based solely on GEBV.
  • The most effective criterion, considering variance over the longest future horizon with the largest reference population, led to a 2% higher genetic level in boars after 20 generations.
  • While benefits diminished with lower accuracy or shorter planning horizons, variance-considering criteria consistently performed as well as or better than GEBV selection without negative side effects on commercial genetic gain.

Conclusions:

  • Selection criteria that account for future genetic variances maintain greater genetic diversity in livestock breeding programs.
  • These variance-considering criteria offer a viable alternative to traditional GEBV selection, providing comparable or improved genetic gain and enhanced genetic variance retention.
  • The proposed criteria are applicable to any genomic breeding program with available phased genotypes, estimated marker effects, and a genetic map.