A genome-wide association study reveals dominance effects on number of teats in pigs

Abstract

Dominance has been suggested as one of the genetic mechanisms explaining heterosis. However, using traditional quantitative genetic methods it is difficult to obtain accurate estimates of dominance effects. With the availability of dense SNP (Single Nucleotide Polymorphism) panels, we now have new opportunities for the detection and use of dominance at individual loci. Thus, the aim of this study was to detect additive and dominance effects on number of teats (NT), specifically to investigate the importance of dominance in a Landrace-based population of pigs. In total, 1,550 animals, genotyped for 32,911 SNPs, were used in single SNP analysis. SNPs with a significant genetic effect were tested for their mode of gene action being additive, dominant or a combination. In total, 21 SNPs were associated with NT, located in three regions with additive (SSC6, 7 and 12) and one region with dominant effects (SSC4). Estimates of additive effects ranged from 0.24 to 0.29 teats. The dominance effect of the QTL located on SSC4 was negative (-0.26 teats). The additive variance of the four QTLs together explained 7.37% of the total phenotypic variance. The dominance variance of the four QTLs together explained 1.82% of the total phenotypic variance, which corresponds to one-fourth of the variance explained by additive effects. The results suggest that dominance effects play a relevant role in the genetic architecture of NT. The QTL region on SSC7 contains the most promising candidate gene: VRTN. This gene has been suggested to be related to the number of vertebrae, a trait correlated with NT.

Figure 1. Genome-wide association study for additive and dominance effects on number of teats in pigs.

On the y-axis is the −log10 (P-values) of single-SNP association with number of teats in pigs. On the x-axis is the physical position of the SNPs across the 18 autosomes. SNPs associated (false discovery rate ≤0.10) with number of teats having additive and dominance effects are represented by squares and triangles, respectively.

Figure 2. Difference in linkage disequilibrium (LD) between two distinct QTL regions.

(a) LD (r2) between the significant SNPs of the QTL region on Sus Scrofa chromosome (SSC) 12; the most significant SNP in this region is surrounded by a square. (b) LD between the SNPs located 0.2 Mb downstream and upstream of the only significant SNP (surrounded by a square) of the QTL region on SSC4. The numbers inside the diamonds are the LD measurements (r²) on a scale of 0 to 100%.

Figure 3. Genotype effects.

Genotype effects and their standard errors of the most significant SNPs on Sus scrofa chromosomes (SSC) 4 and 7 on number of teats (NT). The genotypic effects are relative to the effect of the heterozygous genotype, which was set to zero.