Rare and population-specific functional variation across pig lines

Roger Ros-Freixedes, Bruno D. Valente, Ching-Yi Chen, William O. Herring, Gregor Gorjanc, John M Hickey, Martin Johnsson

Research output: Working paperPreprint


Background It is expected that missense and loss-of-function (LOF) variants are responsible for phenotypic differences among breeds, genetic lines and varieties of livestock and crop species that have undergone diverse selection histories. However, there is still limited knowledge about the existing missense and LOF variation in livestock commercial populations, in particular regarding population-specific variation.

Methods We performed whole-genome re-sequencing of 7,848 individuals from nine commercial pig breeding lines (average coverage: 4.1x) and imputed genotypes for 440,610 pedigree-related individuals. The variants were categorized according to predicted functional annotation (from loss-of-function to intergenic) and prevalence level (number of lines in which the variant segregated; from private to widespread). Variants in each category were examined in terms of distribution along the genome, minor allele frequency, Wright’s fixation index (FST), individual load, and association to production traits.

Results Of the 46 million called variants, 28% were private (i.e., called in only one line) and 21% were widespread (i.e., called in all nine lines). Genomic regions with low recombination rate were enriched with private variants. Low-prevalence variants were enriched for lower allele frequencies, lower FST, and putatively functional and regulatory variants (including loss-of-function and deleterious missense). Only a small subset of low-prevalence variants was found at intermediate allele frequencies and had large estimated effects on production traits. Individuals on average carried less private deleterious missense alleles than expected compared to other predicted consequence types. A small subset of low-prevalence variants with intermediate allele frequencies and higher FST were detected as significantly associated to the production traits and explained small fractions of phenotypic variance (up to 3.2%). These associations were tagged by other more widespread variants, including intergenic variants.

Conclusions Most low-prevalence variants are kept at very low allele frequency and only a small subset contributed detectable fractions of phenotypic variance. Low-prevalence variants are therefore unlikely to hinder across-breed analyses, in particular when predicting genomic breeding values using reference populations of a different genetic background.
Original languageEnglish
Number of pages47
Publication statusPublished - 2 Feb 2022


  • Loss-of-function variants
  • Pig lines
  • Whole Genome Sequencing
  • Genotype imputation
  • Production traits


Dive into the research topics of 'Rare and population-specific functional variation across pig lines'. Together they form a unique fingerprint.

Cite this