Genome‐wide association studies based on sequence‐derived genotypes reveal new QTL associated with conformation and performance traits in the Franches–Montagnes horse breed

Abstract

To identify novel quantitative trait loci (QTL) within horses, we performed genome-wide association studies (GWAS) based on sequence-level genotypes for conformation and performance traits in the Franches-Montagnes (FM) horse breed. Sequence-level genotypes of FM horses were derived by re-sequencing 30 key founders and imputing 50K data of genotyped horses. In total, we included 1077 FM horses genotyped for ~4 million SNPs and their respective de-regressed breeding values of the traits in the analysis. Based on this dataset, we identified a total of 14 QTL associated with 18 conformation traits and one performance trait. Therefore, our results suggest that the application of sequence-derived genotypes increases the power to identify novel QTL which were not identified previously based on 50K SNP chip data.

Morphological and genetic diversity of Pura Raza Español horse with regard to the coat colour

“…Nowadays, the use of sequence‐derived genotype data allows to understand the genetic mechanisms underlying complex traits by increasing the power to detect novel variants. For instance, Frischknecht, Signer‐Hasler, Leeb, Rieder, and Neuditschko () recently confirmed the existence of a genetic association for HW in horses and identified a novel QTL on ECA9 associated with other conformation traits using imputation from sequence data. However, most previous association studies in this species using coat colour as clustering parameter were performed in phenotypes associated with health disorders (Reissmann & Ludwig, ).…”

Genome-Wide Association Studies Based on Equine Joint Angle Measurements Reveal New QTL Affecting the Conformation of Horses

“…Many conformation traits are routinely evaluated during breeding evaluation contests (mare performance tests, field tests, station tests for breeding stallions, etc.) and have been used in breeding value estimation [15,16,17,18,19] and/or genomic analyses, such as genome-wide association studies (GWASs) [20,21]. The heritability (h 2 ) for conformation traits mostly ranges between 0.10 and 0.50 [19].…”

“…However, within the same studies, other conformation traits, such as the traits describing the distal limb, have not shown any significant association to other regions within the equine genome. In the Franches-Montagnes breed, two different GWASs using the same 1077 individuals and phenotypes, once with the 50K single nucleotide polymorphism (SNP) panel [20] and once with sequence derived genotypes [21], could only confirm the QTL (especially for the height at the withers) from the first study. No new loci were significantly associated with the other conformation traits included in both studies, although several, such as neck muscling, were suggestively associated ( p < 10 −6 ) [21].…”

“…In the Franches-Montagnes breed, two different GWASs using the same 1077 individuals and phenotypes, once with the 50K single nucleotide polymorphism (SNP) panel [20] and once with sequence derived genotypes [21], could only confirm the QTL (especially for the height at the withers) from the first study. No new loci were significantly associated with the other conformation traits included in both studies, although several, such as neck muscling, were suggestively associated ( p < 10 −6 ) [21]. This strongly suggests that increased SNP densities are not sufficient to study the genetic variants of the available conformation traits derived from linear description.…”

“…This strongly suggests that increased SNP densities are not sufficient to study the genetic variants of the available conformation traits derived from linear description. The data derived from linear description does not seem to account for the complexity of the conformational phenotypes [21]. In practice the linear scale is often not fully used and skewed towards the perceived optimum [15,17].…”