A Genome-Wide Association Study to Detect QTL for Commercially Important Traits in Swiss Large White Boars

Abstract

The improvement of meat quality and production traits has high priority in the pork industry. Many of these traits show a low to moderate heritability and are difficult and expensive to measure. Their improvement by targeted breeding programs is challenging and requires knowledge of the genetic and molecular background. For this study we genotyped 192 artificial insemination boars of a commercial line derived from the Swiss Large White breed using the PorcineSNP60 BeadChip with 62,163 evenly spaced SNPs across the pig genome. We obtained 26 estimated breeding values (EBVs) for various traits including exterior, meat quality, reproduction, and production. The subsequent genome-wide association analysis allowed us to identify four QTL with suggestive significance for three of these traits (p-values ranging from 4.99×10−6 to 2.73×10−5). Single QTL for the EBVs pH one hour post mortem (pH1) and carcass length were on pig chromosome (SSC) 14 and SSC 2, respectively. Two QTL for the EBV rear view hind legs were on SSC 10 and SSC 16.

Joint QTL mapping and gene expression analysis identify positional candidate genes influencing pork quality traits

“…We have detected genome-wide and chromosome-wide significant QTL for meat quality traits recorded in a Duroc commercial line with a population size that was moderate but comparable to the ones used in other porcine GWAS434445. The limited positional concordance between the set of QTL detected by us and those reported by other authors in purebred populations suggests the existence of a significant amount of genetic heterogeneity for meat quality traits in porcine breeds.…”

“…The genetic determinism of electrical conductivity, acidity and color, which have been often used as predictors of meat quality, has been explored by performing genome-wide association studies (GWAS) in F 2 populations234 as well as in purebred pigs56. An important limitation of using F 2 intercrosses in GWAS studies is that they are not representative of the purebred populations that constitute the selection nuclei of breeding companies.…”

A variant in MYO10 is associated with hind limb conformation in Swiss Large White boars

“…In a previous study, we mapped two QTL for the estimated breeding value for rearview hind legs to SSC 10 and SSC 16 in Swiss Large White boars . The estimated heritability is low and ranges from 0.10 to 0.15 (own unpublished data).…”

“…We used the original discovery cohort consisting of 186 Swiss Large White boars and a new replication cohort of 161 boars from the same breed.…”

Comparison of one-stage and two-stage genome-wide association studies

“…Some animals may have genotypes and EBVs based on information from their relatives, but no direct phenotypes. Although EBVs have been used as dependent variables in GWAS (Becker et al 2013; Johnston et al 2011), this approach has a high false positive rate (Ekine et al 2013). Consequences of using EBVs include varying levels of precision and ‘shrinkage effect’ among the values used to represent phenotypes of different individuals, a reduction in the sample variance of the phenotypes, and ‘double-counting’ of information from relatives (Garrick et al 2009; Ostersen et al 2011).…”