Two-stage selection strategies utilizing marker-quantitative trait locus information and individual performance.

Area of Science:

• Animal breeding and genetics
• Quantitative genetics
• Genomic selection

Background:

• Marker-assisted selection (MAS) offers potential for improving livestock breeding.
• Optimizing MAS strategies requires balancing short-term gains with long-term response and economic viability.

Purpose of the Study:

• To evaluate short- and long-term responses of various two-stage marker-assisted selection strategies in beef cattle.
• To introduce and apply discounted accumulated response for ranking selection strategies.

Main Methods:

• Stochastic simulation of a closed nucleus beef herd.
• Comparison of five second-stage selection strategies including individual phenotype, BLUP, and various marker-QTL indices.
• Application of discounted accumulated response at a 20-year horizon with a 2% inflation rate.

Main Results:

• All strategies moved favorable quantitative trait locus (QTL) alleles towards fixation, with BLUP-based methods being more efficient than mass selection.
• Two-stage selection, particularly using marker-QTL information with BLUP (Strategy 5), significantly increased discounted accumulated response (up to 12%).
• Strategy 5 demonstrated a favorable cost-benefit ratio and reduced inbreeding compared to other methods.

Conclusions:

• Two-stage marker-assisted selection, especially incorporating quantitative trait locus (QTL) information, enhances genetic gain in beef production.
• Discounted accumulated response is a valuable metric for evaluating selection strategies considering time and economic factors.
• Strategy 5 offers an optimal balance of genetic response, cost-effectiveness, and reduced inbreeding for marker-assisted selection.