Genomic selection models for directional dominance: an example for litter size in pigs

Area of Science:

• Animal Genetics
• Quantitative Genetics
• Genomic Selection

Background:

• Quantitative genetics theory links inbreeding depression and heterosis to directional dominance.
• Current genomic selection methods often assume symmetrical dominance effects, potentially overlooking directional influences.

Purpose of the Study:

• To compare methods for incorporating directional dominance in genomic selection.
• To confirm the presence of directional dominance in pig litter size.

Main Methods:

• Evaluated four models: no directional dominance (SN), average homozygosity covariate (SC), skewed Gaussian distributions (AN), and a full model (Full).
• Utilized two pig litter size datasets with extensive genotypic and phenotypic data.

Main Results:

• Models incorporating directional dominance (SC, AN, Full) showed higher probabilities for directional effects than the SN model.
• Predictions of inbreeding depression were higher when directional dominance was considered.
• Model SC, using average individual homozygosity, provided the best fit for the analyzed datasets.

Conclusions:

• Confirmed positive directional dominance for pig litter size, necessitating its inclusion in genomic evaluations.
• Ignoring directional dominance can lead to biased predictions of breeding values and inbreeding depression.
• Recommends using models with non-zero centered Gaussian dominance effects for genomic evaluations.