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Genetics, selection, evolution : GSE2024; 56(1); 45; doi: 10.1186/s12711-024-00914-6

Genomic analyses of withers height and linear conformation traits in German Warmblood horses using imputed sequence-level genotypes.

Abstract: Body conformation, including withers height, is a major selection criterion in horse breeding and is associated with other important traits, such as health and performance. However, little is known about the genomic background of equine conformation. Therefore, the aim of this study was to use imputed sequence-level genotypes from up to 4891 German Warmblood horses to identify genomic regions associated with withers height and linear conformation traits. Furthermore, the traits were genetically characterised and putative causal variants for withers height were detected. Results: A genome-wide association study (GWAS) for withers height confirmed the presence of a previously known quantitative trait locus (QTL) on Equus caballus (ECA) chromosome 3 close to the LCORL/NCAPG locus, which explained 16% of the phenotypic variance for withers height. An additional significant association signal was detected on ECA1. Further investigations of the region on ECA3 identified a few promising candidate causal variants for withers height, including a nonsense mutation in the coding sequence of the LCORL gene. The estimated heritability for withers height was 0.53 and ranged from 0 to 0.34 for the conformation traits. GWAS identified significantly associated variants for more than half of the investigated conformation traits, among which 13 showed a peak on ECA3 in the same region as withers height. Genetic parameter estimation revealed high genetic correlations between these traits and withers height for the QTL on ECA3. Conclusions: The use of imputed sequence-level genotypes from a large study cohort led to the discovery of novel QTL associated with conformation traits in German Warmblood horses. The results indicate the high relevance of the QTL on ECA3 for various conformation traits, including withers height, and contribute to deciphering causal mutations for body size in horses.
© 2024. The Author(s).
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Publication Date: 2024-06-13 PubMed ID: 38872118PubMed Central: 2689269DOI: 10.1186/s12711-024-00914-6Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research investigated the genetic influences on physical characteristics of German Warmblood horses, with a focus on withers height (the horse’s height from shoulder to ground), and identified several genes associated with different conformation traits. The study found a key genetic region, or quantitative trait locus (QTL), on horse chromosome 3, which influences many conformation traits, including withers height.

Research Methods and Study Cohort

  • The researchers used genomic data from a large cohort of German Warmblood horses, numbering up to 4,891 individual horses.
  • The method of studying the genetic basis of horse traits was genomic analyses using imputed sequence-level genotypes. This is like filling in the blanks in the genomic data to provide a more detailed look at the horse’s genome and understand which genetic variations matter for the trait in question.

Genomic Findings and Genetic Characterisation of Traits

  • A Genome-Wide Association Study (GWAS) confirmed a previous understanding about a significant QTL on equine chromosome 3 near the LCORL/NCAPG locus. A locus is a specific place in the genome where a particular gene is found.
  • This QTL explains 16% of the variation in withers height among the horses, a significant finding given that many traits are usually influenced by multiple genetic factors.
  • The study also identified another significant association signal on equine chromosome 1 (ECA1).
  • From the area around the ECA3 QTL, the team identified a number of potential causal genetic variants for the withers height variation, including a nonsense mutation in the coding sequence of the LCORL gene. A nonsense mutation is a genetic alteration that can alter the normal functioning of a gene.

Estimating Heritability and Genetic Correlations

  • The heritability of withers height, that is the variance of this trait that can be explained by genetics, was estimated at 53%.
  • Additionally, various conformation traits showed a range of heritability estimates from 0 to 34%.
  • More than half of the examined conformation traits had notably associated genetic variants. Intriguingly, 13 of these traits were associated with the same QTL on ECA3 as the withers height.
  • From this, they determined that there is a high genetic correlation between these 13 traits and withers height within this QTL on ECA3, meaning that the same genetic factors seemed to influence these traits.

Significance of the Study and Conclusions

  • The use of this large study cohort with their imputed sequence-level genotypes led to the discovery of new QTL associated with different conformation traits in German Warmblood horses.
  • Most significantly, the study shed light on the significant relevance of the QTL on ECA3 for various conformation traits, including withers height. Thus, the study contributes to the understanding of the genetic basis of body size in horses.

Cite This Article

APA
Reich P, Möller S, Stock KF, Nolte W, von Depka Prondzinski M, Reents R, Kalm E, Kühn C, Thaller G, Falker-Gieske C, Tetens J. (2024). Genomic analyses of withers height and linear conformation traits in German Warmblood horses using imputed sequence-level genotypes. Genet Sel Evol, 56(1), 45. https://doi.org/10.1186/s12711-024-00914-6

Publication

Genetics, selection, evolution : GSE
ISSN: 1297-9686
NlmUniqueID: 9114088
Country: France
Language: English
Volume: 56
Issue: 1
Pages: 45

Researcher Affiliations

Reich, Paula
  • Department of Animal Sciences, Georg-August-University Göttingen, 37077, Göttingen, Germany. paula.reich@agr.uni-goettingen.de.
  • Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, 37075, Göttingen, Germany. paula.reich@agr.uni-goettingen.de.
Möller, Sandra
  • Department of Animal Sciences, Georg-August-University Göttingen, 37077, Göttingen, Germany.
Stock, Kathrin F
  • IT Solutions for Animal Production (vit), 27283, Verden, Germany.
Nolte, Wietje
  • Saxon State Office for Environment, Agriculture and Geology, 01468, Moritzburg, Germany.
von Depka Prondzinski, Mario
  • Werlhof Institute, 30159, Hannover, Germany.
Reents, Reinhard
  • IT Solutions for Animal Production (vit), 27283, Verden, Germany.
Kalm, Ernst
  • Institute of Animal Breeding and Husbandry, Kiel University, 24098, Kiel, Germany.
Kühn, Christa
  • Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany.
  • Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059, Rostock, Germany.
  • Friedrich-Loeffler-Institute, 17493, Greifswald - Riems Island, Germany.
Thaller, Georg
  • Institute of Animal Breeding and Husbandry, Kiel University, 24098, Kiel, Germany.
Falker-Gieske, Clemens
  • Department of Animal Sciences, Georg-August-University Göttingen, 37077, Göttingen, Germany.
  • Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, 37075, Göttingen, Germany.
Tetens, Jens
  • Department of Animal Sciences, Georg-August-University Göttingen, 37077, Göttingen, Germany.
  • Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, 37075, Göttingen, Germany.

MeSH Terms

  • Animals
  • Horses / genetics
  • Quantitative Trait Loci
  • Genome-Wide Association Study / methods
  • Genotype
  • Polymorphism, Single Nucleotide
  • Phenotype
  • Male
  • Female

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Citations

This article has been cited 6 times.
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