Landscape of Loci and Candidate Genes for Muscle Fatty Acid Composition in Pigs Revealed by Multiple Population Association Analysis

Abstract

Genome wide association analyses in diverse populations can identify complex trait loci that are specifically present in one population or shared across multiple populations, which help to better understand the genetic architecture of complex traits in a broader genetic context. In this study, we conducted genome-wide association studies and meta-analysis for 38 fatty acid composition traits with 12-19 million imputed genome sequence SNPs in 2446 pigs from six populations, encompassing White Duroc × Erhualian F₂, Sutai, Duroc-Landrace-Yorkshire (DLY) three-way cross, Laiwu, Erhualian, and Bamaxiang pigs that were originally genotyped with 60 K or 1.4 million single nucleotide polymorphism (SNP) chips. The analyses uncovered 285 lead SNPs (P < 5 × 10^-8), among which 78 locate more than 1 Mb to the lead chip SNPs were considered as novel, largely augmented the landscape of loci for porcine muscle fatty acid composition. Meta-analysis enhanced the association significance at loci near FADS2, ABCD2, ELOVL5, ELOVL6, ELOVL7, SCD, and THRSP genes, suggesting possible existence of population shared mutations underlying these loci. Further haplotype analysis at SCD loci identified a shared 3.7 kb haplotype in F₂, Sutai and DLY pigs showing consistent effects of decreasing C18:0 contents in the three populations. In contrast, at FASN loci, we found an Erhualian specific haplotype explaining the population specific association signals in Erhualian pigs. This study refines our understanding on landscape of loci and candidate genes for fatty acid composition traits of pigs.

Keywords: fatty acid composition; genome-wide association studies; meta-analysis; pig; sequence imputation.

Figure 1

Comparison of association strength between imputed and chip SNPs. (A) region for C20:1n-9 on SSC7 in F₂ population; (B) region for C18:1n-9/C16:1n-7 on SSC8 in F₂ population. (C) region for C20:0/C18:0 on SSC5 in Sutai population. (D) region for C20:3n-6/C18:2n-6 on SSC2 in Erhualian population. Imputed and chip SNPs were denoted in blue and red color, respectively. The lead SNPs are marked by triangles.

Figure 2

A combined Manhattan plot for GWAS on fatty acid composition traits across six populations. Genome-wide representation of all lead SNPs identified single population GWAS, which were marked by a colored dot. Results from different populations were represented by different colors. The y axis shows the -log₁₀p-values for association with corresponding fatty acid composition traits and the x axis shows the genomic position of genetic variants. Candidate genes are denoted with different colors, blue for candidate gene previously identified, and red for candidate gene newly found in current study.

Figure 3

Comparison of association strength between signal-population GWAS and Meta-analysis. (A) Associations of SNP in a 4 Mb region on SSC7 for C20:1n-9/C18:1n-9 in Erhualian pigs (blue dots) versus GWAS meta-analysis (red dots). (B) Associations of SNP in an 8 Mb region on SSC8 for C18:1n-9/C16:1n-7 in DLY pigs (blue dots) versus GWAS meta-analysis (red dots). (C) Associations of SNP in an 8 Mb region on SSC14 for C18:0 in DLY pigs (blue dots) versus GWAS meta-analysis (red dots). (D) Associations of SNP in an 8 Mb region on SSC16 for C20:0/C18:0 in DLY pigs (blue dots) versus GWAS meta-analysis (red dots). The lead SNPs were marked with gray diamond.

Figure 4

Haplotype analysis of the major QTL for C18:0 on SSC14 in the F₂, Sutai and DLY populations. (A) The significant regional plots for the SNP that affects the C18:0 content on SSC14 across three populations. (B) Distribution of effects of 41 SNP haplotype centered on the lead SNP for C18:0 identified in DLY pigs. The points represent estimates of the haplotype effects. Vertical bars represented the standard errors of the haplotype effect estimates. Haplotypes that shared the 3.7 kb segment (121,450,788-121,454,457 bp) were highlighted by orange color. (C) Heatmap of haplotypes spans 20kb upstream and downstream (121,434,379-121,473,888 bp) of the lead SNP 14:121,454,019 in individuals that carry Hap3 in F2, Hap4 in Sutai, Hap2, Hap3 and Hap4 in DLY pigs. (D) The detail base pair information of a 7-kb segment than encompassed the 3.7 kb (121,450,788-121,454,457 bp) chromosome segment shared by F₂-Hap3, Sutai-Hap4, DLY-Hap2, DLY-Hap3 and DLY-Hap4 haplotypes.

Figure 5

Haplotype analysis of the major QTL for C14:0 on SSC12 in the EHL populations. (A) Distribution of effects of 41 SNP haplotype centered on the lead SNP for C14:0 (1,482,028-1,483,956 bp) identified in Erhualian pigs in the six populations. The points represent the estimates of the haplotype effects. Vertical bars represented the standard errors of the haplotype effect estimates. Haplotype (Hap4) with significant effect of decreasing C14:0 in Erhualian pigs was highlighted by orange color. (B) Neighbor-joining tree for major haplotypes of the QTL on SSC12 across six populations. Haplotype (Erhualian-Hap4) specific to Erhualian pigs is highlighted by red colors.

Figure 6

Protein-protein interaction network and gene ontology enrichment analysis of candidate genes. (A) Protein-protein interaction network of the 32 most plausible candidate genes of the lead SNPs detected by GWAS and meta-analysis in STRING v10.5 database. (B) Gene ontology enrichment analysis of candidate genes. Over-represented GO/pathway terms were grouped based on kappa statistics. GO/pathway terms are represented as nodes, and the node size represents the term enrichment significance, while the edges represent significant similarity between categories.