Genome-wide association studies for fatty acid metabolic traits in five divergent pig populations

Abstract

Fatty acid composition profiles are important indicators of meat quality and tasting flavor. Metabolic indices of fatty acids are more authentic to reflect meat nutrition and public acceptance. To investigate the genetic mechanism of fatty acid metabolic indices in pork, we conducted genome-wide association studies (GWAS) for 33 fatty acid metabolic traits in five pig populations. We identified a total of 865 single nucleotide polymorphisms (SNPs), corresponding to 11 genome-wide significant loci on nine chromosomes and 12 suggestive loci on nine chromosomes. Our findings not only confirmed seven previously reported QTL with stronger association strength, but also revealed four novel population-specific loci, showing that investigations on intermediate phenotypes like the metabolic traits of fatty acids can increase the statistical power of GWAS for end-point phenotypes. We proposed a list of candidate genes at the identified loci, including three novel genes (FADS2, SREBF1 and PLA2G7). Further, we constructed the functional networks involving these candidate genes and deduced the potential fatty acid metabolic pathway. These findings advance our understanding of the genetic basis of fatty acid composition in pigs. The results from European hybrid commercial pigs can be immediately transited into breeding practice for beneficial fatty acid composition.

Figure 1. Manhattan plots of significant loci for fatty acid metabolic traits in the White Duroc × Erhualian F₂ population.

(a) GWAS results for C16:0, C18:0 and C18:0/C16:0 in abdominal fat; (b) GWAS results for C16:1n7, C18:1n9 and C18:1n9/C16:1n7 in abdominal fat; (c) GWAS results for C18:2n6, C20:2n6 and C20:2n6/C18:2n6 in abdominal fat; (d) GWAS results for C16:1n7, C18:1n9 and C18:1n9/C16:1n7 in longissimus dorsi muscle. Negative log₁₀ P values of the qualified SNPs (N) are plotted against their genomic positions. SNPs on different chromosomes are denoted by different colors. The solid line represents the genome-wide threshold (0.05/N). The dash line indicates the suggestive threshold (1/N).

Figure 2. Manhattan plots of significant loci for fatty acid metabolic traits in the Erhualian, Laiwu and DLY populations.

(a) GWAS results for C18:2n6, C20:3n6 and C20:3n6/C18:2n6 in the Erhualian population; (b) GWAS results for C18:2n6, C20:2n6 and C20:2n6/C18:2n6 in the Erhualian population; (c) GWAS results for C20:3n6, C20:4n6, and C20:4n6/C20:3n6 in the Laiwu population; (d) GWAS results for C16:0, C16:1n7 and C16:1n7/C16:0 in the DLY population; Negative log₁₀ P values of the qualified SNPs (N) are plotted against their genomic positions. SNPs on different chromosomes are denoted by different colors. The solid line represents the genome-wide threshold (0.05/N). The dash line indicates the suggestive threshold (1/N).

Figure 3. Manhattan plot of the GWAS meta-analysis across the five populations.

The associated traits are indicated above the corresponding loci. Negative log₁₀ P values of the qualified SNPs are plotted against their genomic positions. The solid line represents the genome-wide threshold (0.05/N). The dash line indicates the suggestive threshold (1/N). N stands for the common SNPs across the five populations.

Figure 4. Graphical illustration of the potential fatty acid metabolism pathway and plausible candidate genes.

The illustration shows the step-by-step synthesis of fatty acids. Significant loci have been identified for the ratios of substrates to products linked by red arrows. Plausible candidate genes that we highlighted for significant loci in this study are indicated alongside red arrows. For fatty acids linked by blue arrows, the loci for the metabolic ratios between these fatty acids remain unexplored.