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Research article - Peer-reviewed, 2022

Rare and population-specific functional variation across pig lines

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

Abstract

Background It is expected that functional, mainly missense and loss-of-function (LOF), and regulatory variants are responsible for most phenotypic differences between breeds and genetic lines of livestock species that have undergone diverse selection histories. However, there is still limited knowledge about the existing missense and LOF variation in commercial livestock populations, in particular regarding population-specific variation and how it can affect applications such as across-breed genomic prediction. Methods We re-sequenced the whole genome of 7848 individuals from nine commercial pig lines (average sequencing coverage: 4.1x) and imputed whole-genome genotypes for 440,610 pedigree-related individuals. The called variants were categorized according to predicted functional annotation (from LOF 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 their distribution along the genome, alternative allele frequency, per-site Wright's fixation index (F-ST), individual load, and association to production traits. Results Of the 46 million called variants, 28% were private (called in only one line) and 21% were widespread (called in all nine lines). Genomic regions with a low recombination rate were enriched with private variants. Low-prevalence variants (called in one or a few lines only) were enriched for lower allele frequencies, lower F-ST, and putatively functional and regulatory roles (including LOF and deleterious missense variants). On average, individuals carried fewer private deleterious missense alleles than expected compared to alleles with other predicted consequences. Only a small subset of the low-prevalence variants had intermediate allele frequencies and explained small fractions of phenotypic variance (up to 3.2%) of production traits. The significant low-prevalence variants had higher per-site F-ST than the non-significant ones. These associated low-prevalence variants were tagged by other more widespread variants in high linkage disequilibrium, including intergenic variants. Conclusions Most low-prevalence variants have low minor allele frequencies and only a small subset of low-prevalence variants contributed detectable fractions of phenotypic variance of production traits. Accounting for low-prevalence variants is therefore unlikely to noticeably benefit across-breed analyses, such as the prediction of genomic breeding values in a population using reference populations of a different genetic background.

Published in

Genetics Selection Evolution
2022, volume: 54, article number: 39
Publisher: BMC

Authors' information

Ros-Freixedes, Roger
University of Edinburgh
Ros-Freixedes, Roger
Universitat de Lleida
Valente, Bruno
Pig Improvement Company
Chen, Ching-Yi
Pig Improvement Company
Herring, William
Pig Improvement Company
Gorjanc, Gregor
University of Edinburgh
Hickey, John M.
University of Edinburgh
University of Edinburgh
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics

UKÄ Subject classification

Animal and Dairy Science

Publication Identifiers

DOI: https://doi.org/10.1186/s12711-022-00732-8

URI (permanent link to this page)

https://res.slu.se/id/publ/117560