Targeted allele frequency tuning in breeding populations via alternative optimum contribution selection

Area of Science:

• Quantitative genetics
• Population genetics
• Genomic selection

Background:

• Genomic inbreeding management using genomic relationship matrices influences allele frequencies.
• This phenomenon can be leveraged for targeted allele frequency manipulation.

Purpose of the Study:

• To explore the exploitation of allele frequency shifts for purposeful allele frequency changes.
• To introduce and evaluate a novel selection method, Targeted Allele Frequency Tuning (TAFT), for manipulating allele frequencies.
• To assess TAFT's efficacy in purging deleterious alleles and maintaining genetic diversity.

Main Methods:

• Developed and applied the Targeted Allele Frequency Tuning (TAFT) method, integrated with optimal contribution selection (OCS) as TAFT-OCS.
• Validated TAFT-OCS using a simulated dataset and the Friesian horse population.
• Quantified the relationship between the average entry of VanRaden's numerator matrix (ZZ'¯) and the squared difference between population and centering allele frequencies.

Main Results:

• TAFT-OCS effectively shifted allele frequencies towards desired targets, outperforming traditional index methods.
• Demonstrated successful purging of 12 deleterious alleles within approximately 6 generations in the Friesian horse population.
• Achieved significant genetic gain (3.7 cm in withers height per generation) while maintaining a low pedigree inbreeding rate (<0.5%).

Conclusions:

• TAFT-OCS is a novel and effective method for directly altering allele frequencies to desired values, including intermediate frequencies.
• The method is particularly beneficial for managing genetic diversity and purging deleterious alleles.
• TAFT shifts selection focus from individuals to alleles, offering precise control over population allele frequencies.