Abstract
BackgroundBackfat 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.MethodsData 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.ResultsWe 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.ConclusionsOur 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.
Highlights
Backfat thickness is an important carcass composition trait for pork production and is commonly included in swine breeding programmes
Together with the candidate genes that were found in the other genomic regions, the results support the involvement of energy homeostasis, adipogenesis, fatty acid metabolism, and insulin signalling pathways, and suggest the contribution of other metabolic pathways, which are less well understood, to genetic variation for backfat thickness in pigs, such as the phosphate, calcium, and vitamin D homeostasis pathways
Our genome-wide association study (GWAS) results obtained on 275,590 pigs from lines with diverse genetic backgrounds confirmed the polygenic architecture of backfat thickness and the importance of genes associated with energy homeostasis, adipogenesis, fatty acid metabolism, and insulin signalling pathways for fat deposition in pigs
Summary
Backfat thickness is an important carcass composition trait for pork production and is commonly included in swine breeding programmes. Gozalo‐Marcilla et al Genet Sel Evol (2021) 53:76 growth efficiency and lean meat content [2]. This is typically achieved by including backfat thickness in the economic index for selection within pig lines. More than 1400 quantitative trait loci (QTL) related to backfat thickness have been reported (https://www.animalgenome.org/QTLdb). Results from these studies showed that backfat thickness is a polygenic trait that is regulated by a large number of small-effect variants. With the advent of single-nucleotide polymorphism (SNP) genotyping arrays, gene expression analyses, and other high-throughput genotyping technologies, many more candidate genes for backfat thickness have been reported that are involved in very diverse biological functions and metabolic pathways, such as: adipogenesis [13, 14]; lipid metabolism (biosynthesis, absorption, transport, catabolism and homeostasis) pathways, including those related to fatty acids and triglycerides [13, 15, 16]; regulation of feed intake and energy homeostasis, through hormone-mediated responses [17,18,19,20] or even taste perception [21]; the adipocytokine signalling pathway [17, 19]; the vitamin D metabolic pathway [13]; and nervous system development and regulation [22]
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