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Research article - Peer-reviewed, 2021

Genetic architecture and major genes for backfat thickness in pig lines of diverse genetic backgrounds

Gozalo-Marcilla, Miguel; Buntjer, Jaap; Johnsson, Martin; Batista, Lorena; Diez, Federico; Werner, Christian R.; Chen, Ching-Yi; Gorjanc, Gregor; Mellanby, Richard J.; Hickey, John M.; Ros-Freixedes, Roger;

Abstract

Background Backfat thickness is an important carcass composition trait for pork production and is commonly included in swine breeding programmes. In this paper, we report the results of a large genome-wide association study for backfat thickness using data from eight lines of diverse genetic backgrounds. Methods Data comprised 275,590 pigs from eight lines with diverse genetic backgrounds (breeds included Large White, Landrace, Pietrain, Hampshire, Duroc, and synthetic lines) genotyped and imputed for 71,324 single-nucleotide polymorphisms (SNPs). For each line, we estimated SNP associations using a univariate linear mixed model that accounted for genomic relationships. SNPs with significant associations were identified using a threshold of p < 10(-6) and used to define genomic regions of interest. The proportion of genetic variance explained by a genomic region was estimated using a ridge regression model. Results We found significant associations with backfat thickness for 264 SNPs across 27 genomic regions. Six genomic regions were detected in three or more lines. The average estimate of the SNP-based heritability was 0.48, with estimates by line ranging from 0.30 to 0.58. The genomic regions jointly explained from 3.2 to 19.5% of the additive genetic variance of backfat thickness within a line. Individual genomic regions explained up to 8.0% of the additive genetic variance of backfat thickness within a line. Some of these 27 genomic regions also explained up to 1.6% of the additive genetic variance in lines for which the genomic region was not statistically significant. We identified 64 candidate genes with annotated functions that can be related to fat metabolism, including well-studied genes such as MC4R, IGF2, and LEPR, and more novel candidate genes such as DHCR7, FGF23, MEDAG, DGKI, and PTN. Conclusions Our results confirm the polygenic architecture of backfat thickness and the role of genes involved in energy homeostasis, adipogenesis, fatty acid metabolism, and insulin signalling pathways for fat deposition in pigs. The results also suggest that several less well-understood metabolic pathways contribute to backfat development, such as those of phosphate, calcium, and vitamin D homeostasis.

Published in

Genetics Selection Evolution

2021, volume: 53, number: 1, article number: 76
Publisher: BMC

Authors' information

Gozalo-Marcilla, Miguel
University of Edinburgh
Buntjer, Jaap
University of Edinburgh
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
University of Edinburgh
Batista, Lorena
University of Edinburgh
Diez, Federico
University of Edinburgh
Chen, Ching-Yi
Pig Improvement Company
Werner, Christian R.
University of Edinburgh
Gorjanc, Gregor
University of Edinburgh
Mellanby, Richard J.
University of Edinburgh
Hickey, John M.
University of Edinburgh
Ros-Freixedes, Roger
University of Edinburgh

UKÄ Subject classification

Genetics and Breeding

Publication Identifiers

DOI: https://doi.org/10.1186/s12711-021-00671-w

URI (permanent link to this page)

https://res.slu.se/id/publ/113809