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PloS one2019; 14(4); e0215913; doi: 10.1371/journal.pone.0215913

Selection signatures in four German warmblood horse breeds: Tracing breeding history in the modern sport horse.

Abstract: The study of selection signatures helps to find genomic regions that have been under selective pressure and might host genes or variants that modulate important phenotypes. Such knowledge improves our understanding of how breeding programmes have shaped the genomes of livestock. In this study, 942 stallions were included from four, exemplarily chosen, German warmblood breeds with divergent historical and recent selection focus and different crossbreeding policies: Trakehner (N = 44), Holsteiner (N = 358), Hanoverian (N = 319) and Oldenburger (N = 221). Those breeds are nowadays bred for athletic performance and aptitude for show-jumping, dressage or eventing, with a particular focus of Holsteiner on the first discipline. Blood samples were collected during the health exams of the stallion preselections before licensing and were genotyped with the Illumina EquineSNP50 BeadChip. Autosomal markers were used for a multi-method search for signals of positive selection. Analyses within and across breeds were conducted by using the integrated Haplotype Score (iHS), cross-population Extended Haplotype Homozygosity (xpEHH) and Runs of Homozygosity (ROH). Oldenburger and Hanoverian showed very similar iHS signatures, but breed specificities were detected on multiple chromosomes with the xpEHH. The Trakehner clustered as a distinct group in a principal component analysis and also showed the highest number of ROHs, which reflects their historical bottleneck. Beside breed specific differences, we found shared selection signals in an across breed iHS analysis on chromosomes 1, 4 and 7. After investigation of these iHS signals and shared ROH for potential functional candidate genes and affected pathways including enrichment analyses, we suggest that genes affecting muscle functionality (TPM1, TMOD2-3, MYO5A, MYO5C), energy metabolism and growth (AEBP1, RALGAPA2, IGFBP1, IGFBP3-4), embryonic development (HOXB-complex) and fertility (THEGL, ZPBP1-2, TEX14, ZP1, SUN3 and CFAP61) have been targeted by selection in all breeds. Our findings also indicate selection pressure on KITLG, which is well-documented for influencing pigmentation.
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Publication Date: 2019-04-25 PubMed ID: 31022261PubMed Central: PMC6483353DOI: 10.1371/journal.pone.0215913Google Scholar: Lookup
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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.

The article reports a study that investigates how breeding programs have shaped the genomes of four distinct breeds of German warmblood horses: the Trakehner, Holsteiner, Hanoverian, and Oldenburger. Blood samples were analyzed from 942 stallions and compared to detect common ‘selection signatures’, which are regions of the genome that have been specifically targeted by selective breeding.

Selection Signatures

  • The investigation looked for areas of the genome that have historically been under selective pressure during breeding, known as selection signatures. Such areas can host genes that influence key traits.
  • By studying these selection signatures, researchers were able to gain an understanding of the genetic effects of different breeding programmes on the four breeds of German warmblood horses.

Study Methods and Breeds

  • The study included 942 stallions from four German warmblood breeds: Trakehner, Holsteiner, Hanoverian and Oldenburger.
  • These breeds have each been bred with different historical and recent focuses and policies. Each is now predominantly bred for athletic performance, particularly in show-jumping, dressage, or eventing, with the Holsteiner specifically focused on show-jumping.

Data Collection and Analysis

  • Blood samples were obtained during health examinations at the horses’ licensing preselections, and genetic information was extracted.
  • The researchers used several methods to search for signs of positive selection in the horses’ genomes. They used the integrated Haplotype Score (iHS), cross-population Extended Haplotype Homozygosity (xpEHH) and Runs of Homozygosity (ROH).

Findings

  • The Oldenburger and Hanoverian breeds showed similar iHS signatures. However, breed-specific genomic features reflecting divergent selective pressures were detected using xpEHH.
  • The Trakehner breed showed distinct genetic features, clustering separately in a principal component analysis. This breed also exhibited the highest number of ROHs, which echoes its known historical genetic bottleneck.
  • Apart from breed-specific differences, some shared selection signatures were found across breeds, particularly on chromosomes 1, 4 and 7.

Suggested Traits Under Selection

  • Upon analyzing these selection signatures, it is suggested that genes influencing muscle function, energy metabolism and growth, embryonic development, and fertility have been major targets of selective breeding across all the breeds studied.
  • The study also suggests a selection pressure on pigmentation, indicated by the presence of the known pigmentation-related gene KITLG.

Cite This Article

APA
Nolte W, Thaller G, Kuehn C. (2019). Selection signatures in four German warmblood horse breeds: Tracing breeding history in the modern sport horse. PLoS One, 14(4), e0215913. https://doi.org/10.1371/journal.pone.0215913

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 14
Issue: 4
Pages: e0215913

Researcher Affiliations

Nolte, Wietje
  • Institute of Genome Biology, Leibniz-Institute for Farm Animal Biology, Dummerstorf, Germany.
Thaller, Georg
  • Institute for Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Kiel, Germany.
Kuehn, Christa
  • Institute of Genome Biology, Leibniz-Institute for Farm Animal Biology, Dummerstorf, Germany.
  • Faculty of Agricultural and Environmental Science, University of Rostock, Rostock, Germany.

MeSH Terms

  • Alleles
  • Animals
  • Breeding
  • Genome
  • Genotype
  • Germany
  • Haplotypes / genetics
  • Homozygote
  • Horses / genetics
  • Molecular Sequence Annotation
  • Principal Component Analysis
  • Selection, Genetic
  • Sports

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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