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Scientific reports2019; 9(1); 6095; doi: 10.1038/s41598-019-42640-w

The horse Y chromosome as an informative marker for tracing sire lines.

Abstract: Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski's horses. Among domestic horses we confirmed the predominance of a young'crown haplogroup' in Central European and North American breeds. Within the crown, we distinguished 58 haplotypes based on 211 variants, forming three major haplogroups. In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse. In a genealogical showcase, we distinguished the patrilines of the three English Thoroughbred founder stallions and resolved a historic controversy over the parentage of the horse 'Galopin', born in 1872. We observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication 5,500 years ago.
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Publication Date: 2019-04-15 PubMed ID: 30988347PubMed Central: PMC6465346DOI: 10.1038/s41598-019-42640-wGoogle 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 research conducted Y-chromosome investigations on horses to reveal paternal lineages and explore the ancestry of sire lines. Findings indicate three main haplogroups among domestic horses, contributing to the identification of specific patrilines and resolving historical discrepancies in horses’ parentage.

Methodology

  • The researchers de novo assembled a draft reference of the male-specific region of the Y chromosome using Illumina short reads. This method involves building genome sequences from scratch, without guidance from a reference genome. It’s particularly useful in studying species or individuals for which no reference genome exists or to detect significant structural variants.
  • The team screened 5.8 million base pairs for variations in 130 specimens. These included horses from intensively selected breeds, rural breeds, and nine Przewalski’s horses, which are a rare and endangered subspecies of wild horse.

Results

  • The study confirmed the predominance of a relatively young ‘crown haplogroup’ in Central European and North American breeds. A haplogroup is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation. In this case, the ‘crown’ refers to the most recent common ancestor of a particular group.
  • The team distinguished 58 haplotypes based on 211 variants. These formed three major haplogroups among domestic horses. A Haplotype is a group of genes within an organism that was inherited together from a single parent.
  • Two of these groups had been previously characterised: one observed in Arabian/Coldblooded horses, and the other in Turkoman/Thoroughbred horses. The newly uncovered third group contained Iberian lines and a North African Barb Horse, expanding our understanding of sire lines in different breeds.

Genealogical Showcase

  • The researchers successfully distinguished the patrilines of the three English Thoroughbred founder stallions. This not only verifies the effectiveness of their Y-chromosomal haplotyping approach but also highlights its utility in practical horse breeding and lineage verification scenarios.
  • The study resolved a longstanding controversy over the parentage of the horse ‘Galopin,’ born in 1872, by identifying its appropriate lineage through the analysis of Y-chromosomal lineages.

Historical Radiations

  • The study observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication around 5,500 years ago. These ‘radiations’ indicate periods when species rapidly diversify in a relatively short amount of time, relating here to the spread and variety in horse breeds after the advent of domestication.

Cite This Article

APA
Felkel S, Vogl C, Rigler D, Dobretsberger V, Chowdhary BP, Distl O, Fries R, Jagannathan V, Janečka JE, Leeb T, Lindgren G, McCue M, Metzger J, Neuditschko M, Rattei T, Raudsepp T, Rieder S, Rubin CJ, Schaefer R, Schlötterer C, Thaller G, Tetens J, Velie B, Brem G, Wallner B. (2019). The horse Y chromosome as an informative marker for tracing sire lines. Sci Rep, 9(1), 6095. https://doi.org/10.1038/s41598-019-42640-w

Publication

Scientific reports
ISSN: 2045-2322
NlmUniqueID: 101563288
Country: England
Language: English
Volume: 9
Issue: 1
Pages: 6095

Researcher Affiliations

Felkel, Sabine
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria.
  • Vienna Graduate School of Population Genetics, Vienna, Austria.
Vogl, Claus
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria.
Rigler, Doris
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria.
Dobretsberger, Viktoria
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria.
Chowdhary, Bhanu P
  • United Arab Emirates University, 15551, Al Ain, UAE.
Distl, Ottmar
  • Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, 30559, Germany.
Fries, Ruedi
  • Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, Freising, 85354, Germany.
Jagannathan, Vidhya
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.
Janečka, Jan E
  • Department of Biological Sciences, Duquesne University, Pittsburgh, 15282, USA.
Leeb, Tosso
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.
Lindgren, Gabriella
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden.
  • Department of Biosystems, KU Leuven, Leuven, 3001, Belgium.
McCue, Molly
  • Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, 55108, USA.
Metzger, Julia
  • Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, 30559, Germany.
Neuditschko, Markus
  • Agroscope, Swiss National Stud Farm, Avenches, 1580, Switzerland.
Rattei, Thomas
  • Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
Raudsepp, Terje
  • Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4458, USA.
Rieder, Stefan
  • Agroscope, Swiss National Stud Farm, Avenches, 1580, Switzerland.
Rubin, Carl-Johan
  • Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, 75123, Sweden.
Schaefer, Robert
  • Agroscope, Swiss National Stud Farm, Avenches, 1580, Switzerland.
Schlötterer, Christian
  • Institut fuer Populationsgenetik, University of Veterinary Medicine Vienna, Vienna, 1210, Austria.
Thaller, Georg
  • Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, 24098, Germany.
Tetens, Jens
  • Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, 24098, Germany.
  • Functional Breeding Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, 37077, Germany.
Velie, Brandon
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden.
  • School of Life and Environmental Sciences, University of Sydney, Sydney, 2006, Australia.
Brem, Gottfried
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria.
Wallner, Barbara
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria. barbara.wallner@vetmeduni.ac.at.

MeSH Terms

  • Animals
  • Breeding
  • Domestication
  • Female
  • Genetic Variation
  • Haplotypes
  • Horses / genetics
  • Male
  • Pedigree
  • Phylogeny
  • Y Chromosome / genetics

Grant Funding

  • W 1225 / Austrian Science Fund FWF

Conflict of Interest Statement

The authors declare no competing interests.

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