Allele frequency changes due to hitch-hiking in genomic selection programs.

Area of Science:

• Animal Breeding and Genetics
• Quantitative Genetics
• Genomics

Background:

• Genomic selection (GS) can reduce pedigree-based inbreeding compared to best linear unbiased prediction (BLUP).
• Pedigree inbreeding may not accurately reflect genetic variation loss or true inbreeding levels due to allele frequency shifts and hitch-hiking.
• Understanding long-term GS impacts on allele frequencies, genetic variation, and inbreeding is crucial.

Purpose of the Study:

• To investigate the effects of long-term genomic selection on allele frequencies, genetic variation, and inbreeding.
• To compare different genomic selection methods regarding their impact on genetic parameters.
• To assess the effectiveness of various selection criteria in controlling inbreeding and preserving genetic diversity.

Main Methods:

• Simulated selection over 25 generations in a population of 400 animals.
• Evaluated six genetic models with varying heritabilities and quantitative trait loci (QTL) numbers.
• Compared four selection criteria: own phenotype, BLUP, genomic BLUP, and Bayesian Lasso for estimated breeding values (EBV).

Main Results:

• Hitch-hiking effects near QTL were more pronounced with higher selection accuracy and fewer QTL.
• Genomic BLUP EBV reduced pedigree inbreeding more than phenotype BLUP EBV, but results varied when using runs of homozygosity.
• Bayesian Lasso EBV demonstrated less genetic drift, reduced favorable allele loss, and better control of both pedigree and genomic inbreeding compared to genomic BLUP.

Conclusions:

• Hitch-hiking effects significantly influence neutral variation, independent of genetic drift.
• Implementing genomic selection requires robust strategies for controlling inbreeding due to substantial hitch-hiking effects.
• Bayesian Lasso emerges as a superior method for managing genetic diversity and inbreeding in long-term genomic selection programs.