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PloS one2013; 8(4); e60015; doi: 10.1371/journal.pone.0060015

Identification of genetic variation on the horse y chromosome and the tracing of male founder lineages in modern breeds.

Abstract: The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most widespread HT1 is ancestral and the other five haplotypes apparently arose on the background of HT1 by mutation or gene conversion after domestication. Two haplotypes (HT2 and HT3) are widely distributed at high frequencies among modern European horse breeds. Using pedigree information, we trace the distribution of Y-haplotype diversity to particular founders. The mutation leading to HT3 occurred in the germline of the famous English Thoroughbred stallion "Eclipse" or his son or grandson and its prevalence demonstrates the influence of this popular paternal line on modern sport horse breeds. The pervasive introgression of Thoroughbred stallions during the last 200 years to refine autochthonous breeds has strongly affected the distribution of Y-chromosomal variation in modern horse breeds and has led to the replacement of autochthonous Y chromosomes. Only a few northern European breeds bear unique variants at high frequencies or fixed within but not shared among breeds. Our Y-chromosomal data complement the well established mtDNA lineages and document the male side of the genetic history of modern horse breeds and breeding practices.
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Publication Date: 2013-04-03 PubMed ID: 23573227PubMed Central: PMC3616054DOI: 10.1371/journal.pone.0060015Google 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.

This research focuses on studying the Y chromosome in modern domestic horses. It attempts to trace the paternal lineages in horse breeds via identifying genetic variations. Through high throughput sequencing technology, the study finds a low level of nucleotide variability in horse Y chromosomes, leading to six distinct haplotypes. Out of these, five are considered to have arisen after domestication. The study also links certain haplotypes to popular paternal lines in modern sport horse breeds.

Background of the Research

  • The study is driven by curiosity about population genetic history, specifically as traced through the father’s line, which is represented in the Y chromosome.
  • Despite the existence of abundant diversity in mitochondrial DNA—which is inherited maternally—in modern horses, previous studies had not detected significant sequence diversity in Y-chromosomal DNA.

Methods Used in the Study

  • The researchers used high throughput sequencing technology, a method that allows for quick and efficient identification of genetic sequences.
  • The identified Y-chromosomal markers, which are nucleotide sequences of the DNA that differ among individuals, were used to trace paternal lines.

Results of the Study

  • They found that the nucleotide variability of the modern horse Y chromosome is extremely low, leading to six particular haplotypes, labeled HT1 through HT6.
  • All these haplotypes were found to be distinct from the Przewalski horse, a subspecies of wild horse.
  • The most widespread haplotype, HT1, is believed to be ancestral, i.e., it was shared by initial domesticated horses. The other five haplotypes are thought to have arisen through mutation or gene conversion, a process by which one DNA sequence replaces another, after domestication.

Implications of the Study

  • The mutations leading to new haplotypes are linked to influential paternal lines in modern sport horse breeds. For instance, HT3 is linked with the famous English Thoroughbred stallion “Eclipse.”
  • The study also found that the widespread introgression, the transfer of genetic information from one species to another, of Thoroughbred stallions over the past 200 years has significantly influenced Y-chromosomal variation in modern horse breeds. This has led to the replacement of local Y chromosomes.
  • The study presents significant findings regarding the male side of the genetic history of modern horse breeds and breeding practices, complementing existing knowledge on the mtDNA lineages that document the female side.

Cite This Article

APA
Wallner B, Vogl C, Shukla P, Burgstaller JP, Druml T, Brem G. (2013). Identification of genetic variation on the horse y chromosome and the tracing of male founder lineages in modern breeds. PLoS One, 8(4), e60015. https://doi.org/10.1371/journal.pone.0060015

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 8
Issue: 4
Pages: e60015
PII: e60015

Researcher Affiliations

Wallner, Barbara
  • Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria. barbara.wallner@vetmeduni.ac.at
Vogl, Claus
    Shukla, Priyank
      Burgstaller, Joerg P
        Druml, Thomas
          Brem, Gottfried

            MeSH Terms

            • Animals
            • Breeding
            • Europe
            • Founder Effect
            • Gene Frequency
            • Haplotypes
            • High-Throughput Nucleotide Sequencing
            • Horses / genetics
            • Male
            • Microsatellite Repeats
            • Molecular Sequence Data
            • Pedigree
            • Phylogeny
            • Polymorphism, Single Nucleotide
            • Sequence Analysis, DNA
            • Y Chromosome

            Conflict of Interest Statement

            The authors have declared that no competing interests exist.

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