Testing frequency-based methods of genic selection in addition to genomic selection in goats

Area of Science:

• Animal breeding and genetics
• Quantitative genetics
• Genomic selection

Background:

• Genic selection is a tool in breeding schemes that can impact genetic gain and inbreeding.
• Assigning economic values to genes for genic selection can be challenging due to uncertainty.
• Existing breeding schemes require methods for genic selection that balance genetic gain and inbreeding without precise economic valuations.

Purpose of the Study:

• To propose and evaluate a genic selection method that operates without assigning economic values to individual genes.
• To optimize genic selection within user-defined constraints for genetic gain and inbreeding rates.
• To assess the effectiveness of this method in a practical breeding program with uncertain economic assessments.

Main Methods:

• Developed a genic selection framework constrained by maximum annual genetic gain and inbreeding rates.
• Investigated five methods for increasing favorable allele frequencies via genic selection.
• Applied simulated annealing to optimize sire contributions for favorable allele frequency in progeny.
• Tested the methods on a French Saanen goat breeding dataset involving six genes.

Main Results:

• Substantial genic responses were observed for three out of six genes studied.
• Limited or no response was seen for other genes due to high initial favorable allele frequencies or unfavorable gene associations.
• The proposed method demonstrated the potential for significant allele frequency optimization under defined constraints.
• Negative responses were prevented, adhering to breeding scheme objectives.

Conclusions:

• The developed genic selection method is effective for optimizing allele frequencies without precise economic valuations.
• This approach offers a practical solution for breeding organizations facing uncertainty in gene economic assessment.
• The method can be integrated into existing breeding schemes to manage genetic gain and inbreeding effectively.