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

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

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 signifcant associations were identifed using a threshold of p< 10–6 and used to defne genomic regions of interest. The proportion of genetic variance explained by a genomic region was estimated using a ridge regression model. Results: We found signifcant 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 signifcant. We identifed 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 confrm 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.

• Language: English
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2021
• Number of pages: Str. 1-14
• Numbering: Vol. 53, art. 76
• PID: 20.500.12556/RUL-132567
• UDC: 636.4:575
• ISSN on article: 1297-9686
• DOI: 10.1186/s12711-021-00671-w
• COBISS.SI-ID: 82703363
• Publication date in RUL: 29.10.2021

Record is a part of a journal

• Title: Genetics selection evolution
• Shortened title: Genet. sel. evol.
• Publisher: Springer Nature
• ISSN: 1297-9686
• COBISS.SI-ID: 3183636

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
• Licensing start date: 22.09.2021

Secondary language

• Language: Slovenian
• Keywords: prašiči, genetika, geni, debelina hrbtne slanine