Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds

Barbara Wallner, Claus Vogl, Priyank Shukla, Joerg P Burgstaller, Thomas Druml, Gottfried Brem

Research output: Contribution to journalArticle

40 Citations (Scopus)

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.
LanguageEnglish
Pagese60015
JournalPLoS ONE
Volume8
Issue number4
DOIs
Publication statusPublished - 3 Apr 2013

Fingerprint

horse breeds
Y Chromosome
Y chromosome
Chromosomes
Horses
haplotypes
breeds
Mitochondrial DNA
horses
genetic variation
stallions
Haplotypes
Gene Conversion
mitochondrial DNA
Equus przewalskii
Sports
mutation
gene conversion
livestock breeding
Nucleotides

Keywords

  • SNP-Calling
  • Genetic variation
  • High throughput sequencing
  • Population genetics

Cite this

Wallner, Barbara ; Vogl, Claus ; Shukla, Priyank ; Burgstaller, Joerg P ; Druml, Thomas ; Brem, Gottfried. / Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds. In: PLoS ONE. 2013 ; Vol. 8, No. 4. pp. e60015.
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Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds. / Wallner, Barbara; Vogl, Claus; Shukla, Priyank; Burgstaller, Joerg P; Druml, Thomas; Brem, Gottfried.

In: PLoS ONE, Vol. 8, No. 4, 03.04.2013, p. e60015.

Research output: Contribution to journalArticle

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