Rare and population-specific functional variation across pig lines.

Area of Science:

• Genomics
• Animal Breeding
• Population Genetics

Background:

• Functional variants, including missense and loss-of-function (LOF), are crucial for phenotypic differences in livestock due to selection histories.
• Limited knowledge exists on missense and LOF variation in commercial livestock, particularly population-specific variants and their impact on genomic prediction.

Purpose of the Study:

• To characterize missense and LOF variation in commercial pig populations.
• To assess the impact of population-specific variants on production traits and across-breed genomic prediction.

Main Methods:

• Whole-genome re-sequencing of 7848 pigs from nine commercial lines, with imputation for 440,610 related individuals.
• Categorization of variants by functional annotation and prevalence (private to widespread).
• Analysis of variant distribution, allele frequency, F_ST, individual load, and association with production traits.

Main Results:

• 28% of 46 million variants were private to a single line; 21% were widespread across all nine lines.
• Low-prevalence variants were enriched in regions of low recombination, had lower allele frequencies and F_ST, and included putatively functional/regulatory roles.
• A small subset of low-prevalence variants with intermediate frequencies explained minor fractions of phenotypic variance (up to 3.2%) for production traits.

Conclusions:

• Most low-prevalence variants exhibit low minor allele frequencies and contribute minimally to phenotypic variance.
• Incorporating low-prevalence variants is unlikely to significantly enhance across-breed genomic prediction models, especially when reference populations differ genetically.