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Journal of applied genetics2022; 63(2); 369-378; doi: 10.1007/s13353-021-00681-w

Genetic and genomic characterization followed by single-step genomic evaluation of withers height in German Warmblood horses.

Abstract: Reliability of genomic predictions is influenced by the size and genetic composition of the reference population. For German Warmblood horses, compilation of a reference population has been enabled through the cooperation of five German breeding associations. In this study, preliminary data from this joint reference population were used to genetically and genomically characterize withers height and to apply single-step methodology for estimating genomic breeding values for withers height. Using data on 2113 mares and their genomic information considering about 62,000 single nucleotide polymorphisms (SNPs), analysis of the genomic relationship revealed substructures reflecting breed origin and different breeding goals of the contributing breeding associations. A genome-wide association study confirmed a known quantitative trait locus (QTL) for withers height on equine chromosome (ECA) 3 close to LCORL and identified a further significant peak on ECA 1. Using a single-step approach with a combined relationship matrix, the estimated heritability for withers height was 0.31 (SE = 0.08) and the corresponding genomic breeding values ranged from - 2.94 to 2.96 cm. A mean reliability of 0.38 was realized for these breeding values. The analyses of withers height showed that compiling a reference population across breeds is a suitable strategy for German Warmblood horses. The single-step method is an appealing approach for practical genomic prediction in horses, because not many genotypes are available yet and animals without genotypes can by this way directly contribute to the estimation system.
© 2022. The Author(s).
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Publication Date: 2022-01-14 PubMed ID: 35028913PubMed Central: PMC8979901DOI: 10.1007/s13353-021-00681-wGoogle Scholar: Lookup
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Summary

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The research paper analyses the withers height in German Warmblood horses using genomic data to establish the reliability of genomic predictions. The study confirms a known quantitative trait locus (QTL) for withers height and uncovers a new significant peak on an equine chromosome, concluding that a single-step approach is effective for such genomic prediction in horses.

Study Background

  • The researchers used a collection of genetic data known as a reference population, to conduct their study. For the German Warmblood horses, this reference population was developed through the collaboration of five German breeding associations.
  • The study aimed to utilise this data to understand the genetic and genomic characteristics affecting withers height—a measurement from the ground to the top of the shoulders in horses—and apply a single-step methodology to estimate genomic breeding values for such height.

Data Used and Study Findings

  • The study used data of 2113 mares and approximately 62,000 single nucleotide polymorphisms (SNPs)—units of genetic variation among individuals. The analysis of this data revealed substructures in the genomic relationship reflecting different breeds’ origins and varied breeding goals of the relevant associations.
  • A genome-wide association study performed as an integral part of the research, confirmed a known quantitative trait locus (QTL) for withers height in equine chromosome (ECA) 3 and identified a previously unknown significant peak on ECA 1.
  • Through a single-step approach with a combined relationship matrix, the study estimates the heritability—the proportion of observed variation in a particular trait that can be attributed to inherited genetic factors—for withers height to be 0.31 (SE = 0.08).
  • The corresponding genomic breeding values—the predicted genetic merits of an individual as a genetic parent—ranged from - 2.94 to 2.96 cm. The research yielded a mean reliability of 0.38 for these breeding values.

Conclusions and Implications

  • From the analysis of withers height, the study concluded that compiling a reference population across breeds is a fitting strategy for German Warmblood horses.
  • The single-step method is considered beneficial for viable genomic prediction in horses, particularly considering that not many genotypes—groups of organisms sharing a specific genetic constitution—are available yet.

The paper suggests that organisms without genotypes can now contribute directly to the estimation system with the aid of this approach.

Cite This Article

APA
Vosgerau S, Krattenmacher N, Falker-Gieske C, Seidel A, Tetens J, Stock KF, Nolte W, Wobbe M, Blaj I, Reents R, Kühn C, von Depka Prondzinski M, Kalm E, Thaller G. (2022). Genetic and genomic characterization followed by single-step genomic evaluation of withers height in German Warmblood horses. J Appl Genet, 63(2), 369-378. https://doi.org/10.1007/s13353-021-00681-w

Publication

Journal of applied genetics
ISSN: 2190-3883
NlmUniqueID: 9514582
Country: England
Language: English
Volume: 63
Issue: 2
Pages: 369-378

Researcher Affiliations

Vosgerau, Sarah
  • Institute of Animal Breeding and Husbandry, Kiel University, Olshausenstr. 40, 24098, Kiel, Germany. svosgerau@tierzucht.uni-kiel.de.
Krattenmacher, Nina
  • Institute of Animal Breeding and Husbandry, Kiel University, Olshausenstr. 40, 24098, Kiel, Germany.
Falker-Gieske, Clemens
  • Department of Animal Science, University of Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany.
Seidel, Anita
  • Institute of Animal Breeding and Husbandry, Kiel University, Olshausenstr. 40, 24098, Kiel, Germany.
Tetens, Jens
  • Department of Animal Science, University of Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany.
  • Center for Integrated Breeding Research (CiBreed), University of Göttingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany.
Stock, Kathrin F
  • IT Solutions for Animal Production (Vit), Heinrich-Schroeder-Weg 1, 27283, Verden, Germany.
  • Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Buenteweg 17, 30559, Hannover, Germany.
Nolte, Wietje
  • Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
  • Saxon State Office for Environment, Agriculture and Geology, Schlossallee 1, 01468, Moritzburg, Germany.
Wobbe, Mirell
  • IT Solutions for Animal Production (Vit), Heinrich-Schroeder-Weg 1, 27283, Verden, Germany.
  • Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Buenteweg 17, 30559, Hannover, Germany.
Blaj, Iulia
  • Institute of Animal Breeding and Husbandry, Kiel University, Olshausenstr. 40, 24098, Kiel, Germany.
Reents, Reinhard
  • IT Solutions for Animal Production (Vit), Heinrich-Schroeder-Weg 1, 27283, Verden, Germany.
Kühn, Christa
  • Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
  • Faculty of Agricultural and Environmental Sciences, University Rostock, Justus-von-Liebig-Weg 6, 18059, Rostock, Germany.
von Depka Prondzinski, Mario
  • Werlhof-Institut MVZ, Schillerstr. 23, 30159, Hannover, Germany.
Kalm, Ernst
  • Institute of Animal Breeding and Husbandry, Kiel University, Olshausenstr. 40, 24098, Kiel, Germany.
Thaller, Georg
  • Institute of Animal Breeding and Husbandry, Kiel University, Olshausenstr. 40, 24098, Kiel, Germany.

MeSH Terms

  • Animals
  • Female
  • Genome-Wide Association Study
  • Genomics / methods
  • Genotype
  • Horses / genetics
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci
  • Reproducibility of Results

Conflict of Interest Statement

The authors declare no competing interests.

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Citations

This article has been cited 1 times.
  1. Nolte W, Alkhoder H, Wobbe M, Stock KF, Kalm E, Vosgerau S, Krattenmacher N, Thaller G, Tetens J, Kühn C. Replacement of microsatellite markers by imputed medium-density SNP arrays for parentage control in German warmblood horses.. J Appl Genet 2022 Dec;63(4):783-792.
    doi: 10.1007/s13353-022-00725-9pubmed: 36173533google scholar: lookup
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