Efficiency of direct selection on quantitative trait loci for a two-trait breeding objective

Area of Science:

• Quantitative genetics
• Animal breeding
• Statistical genetics

Background:

• Traditional selection methods rely on phenotypic values, which can be imprecise for complex traits.
• Selection on known quantitative trait loci (DSQ) offers a potential alternative for improving selection accuracy.
• Understanding the relative efficiency of DSQ versus index selection is crucial for optimizing breeding programs.

Purpose of the Study:

• To compare the selection efficiency of DSQ against traditional index selection for single and two-trait objectives.
• To evaluate the impact of trait correlations on the relative performance of DSQ.
• To assess the long-term genetic response and potential drawbacks of DSQ, such as allele fixation.

Main Methods:

• Simulations were conducted using one and ten identified quantitative trait loci (QTL).
• Additive genetic variance was fully accounted for by the simulated QTL.
• Selection efficiency was measured by relative selection efficiency (RSE) and genetic response over generations.

Main Results:

• DSQ demonstrated higher selection efficiency than index selection for two-trait objectives, particularly with negative genetic and phenotypic correlations.
• For a single locus, RSE was 1.11; for ten loci, RSE ranged from 1.5 to 1.8 in early generations but declined over time.
• DSQ led to rapid allele fixation (around 7 generations), while index selection showed a more sustained response up to 15 generations.

Conclusions:

• DSQ is more efficient for multi-trait selection, especially when traits are negatively correlated, but carries the risk of premature fixation of alleles.
• While DSQ provides a strong initial response, index selection may yield comparable or superior cumulative genetic gains over longer periods.
• The fixation of less favorable alleles in DSQ, particularly those with opposing effects on traits, limits the achievement of the economically optimum genotype.