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.
Highlights
Dominance effects are non-additive effects due to the interaction between alleles at the same locus
This last step was necessary because this study focused on both additive and dominance effects and observations were necessary in all three genotype classes
The estimated effects for sex showed that males presented 0.3560.09 more teats than females
Summary
Dominance effects are non-additive effects due to the interaction between alleles at the same locus. Estimates of dominance effects have not been widely used in livestock breeding because it is difficult to estimate these effects accurately based on pedigree [6]. Genomic selection or genome-wide association studies (GWAS) mainly focused on additive genetic effects and ignored dominance. A number of studies investigated the importance of non-additive effects in genomic prediction [6,7,8,9] and GWAS [10,11], showing that accounting for these effects increased the accuracy and reduced the bias of genomically-predicted breeding values in comparison to an additive model [6,7,8,9]. Su et al [9] showed that in a purebred Duroc population the dominance variance accounted for 6% of the total phenotypic variance in daily gain, emphasizing the relevance of dominance
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