Genetic characterisation of stallion lines using Ychromosomal markers
World Breeding Federation for Sport Horses
General Assembly and Seminar
October 18th-20th2015, in Vienna, Austria
Barbara Wallner
Institute of Animal Breeding and Genetics
University of Veterinary medicine, Vienna
Barbara Wallner
Introduction
Famous Influential stallions-indication from the pedigrees
Darley Arabian
Byerley Turk
Godolphin Barb
Kuhailian Haifi
Traveler
Njal
Hárekur frá Geitaskarði Siglavy Bagdady
Prince of Thule
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In most modern horse breeds only a limited number of male lineages are preserved
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Particular founder stallions contributed excessively to today´s breeds
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The influential founders often derive from distant geographical regions
Thoroughbred
Spanish horse
Arabian
Barbara Wallner
Introduction
Tracing of Lipizzan stallion lines
18th century - establishment of the classical
Lipizzan stallion lines
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PLUTO (*1765) – Fredriksborger, Denmark
CONVERSANO (*1767) – Neapolitan Horse, Italy
NEAPOLITANO (*1790) – Neapolitan Horse, Italy
FAVORY (*1779) – Kladrub, Czech Republic
MAESTOSO (*1773) – Father Neapolitan Horse, Kladrub
SIGLAVY (*1810 ) – Original Arabian
TULIPAN (*1800) – Terezovac, Croatia
INCITATO (*1802) – Bethlen, Romania
Barbara Wallner
..so far - information about the origin of influential founders relies only on written records.....
Goals:
Discriminate the founder stallions genetically
- to reveal insight into their origin
- to monitor the influence of certain stallion lines
Barbara Wallner
Genome Horse
64 Chromosomes
2,8 x 2 Gigabases
Barbara Wallner
Mode of inheritance: Autosomal, Y and mtDNA Genome
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♂
Barbara Wallner
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Interpreting Y-chromosomal networks
Y2
Common ancestor
Y1
Past
Median joining network
Y-chrosomale Haplotypes cattle
Katanen et al. 2009
Line 1
Line 2
Line 3
Line 4
Present
Which Y-chromosomal haplotypes are present in a breed?
How are the Y-chromosomal haplotypes related?
Barbara Wallner
With Y-chromosmal markers we can:
• Describe population structures in a breed
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stallion mediated geneflow flow between breeds
number of popular founders
investigate the origin of the stallion lines and their relationship
• Forensic application
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Inspection of deep-rooting paternal pedigrees
BUT: Y-chromosmal markers cannot:
- give information on the breeding value of a horse
- tell anything about the level of inbreeding of a horse
Barbara Wallner
mtDNA and Y-chromosomal lineages in horses
maternal
Cieslak et al. 2010 PlosONE
Vila et al. 2001 Science
Achilli et al. 2012 PNAS
Lippold et al. 2012 BMC
paternal
Wallner et al. 2003 Anim Genet
Lindgren et al. 2004 Nature Genet
Wallner et al. 2004 J of Hered
Brandariz-Fontes et al. 2013 PlosONE
„Maternal and paternal lines often display a totally different story, which is
clearly evident in the domestic horse.“
Lindgren et al., NatGen 2004
Barbara Wallner
High throughput sequencing technology
high throughput sequencing enables the
sequencing „reading“ of a complete
mammalian genome within a few days
2009 Genome sequence of
„Twilight“ finished
2012 we started high throughput
sequencing on the horse Y-chromosome
Barbara Wallner
Screening for Y-chromosomal variants
Sequence 186kb from the Y-chromosome
9 domestic horses from different breeds
Arabian, Shagya-Arabian
Thoroughbred, Trakehner, Quarter Horse
Shire Horse
Icelandic Horse
Norwegian Fjord
Shetland Pony
8 Lipizzan horses
Przewalski horse
Network of the Haplotypes identified in 17 domestic horses
and in the Przewalski horse
Norwegian Fjord
Shetland pony
English Thoroughbred
HT5
966 bp dele on
Icelandic horse Gene conversion
HT4
A <- G
Muta on
HT1
T -> A
T -> HT2
Muta on
Puta ve
gene conversion
37 SNPs and 3051 bp dele on
HTprz1
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.
doi:10.1371/journal.pone.0060015
HT3
Geographical distribution of Y-haplotypes
A
Icelandic horse
Norwegian Fjord
Shetland pony
American breeds
Appaloosa
Paint Horse
Welsh
Russian Arabian
English
Thoroughbred
Haflinger
Pinto
Shagya Arabian
Noric
Quarter horse
Lipizzan
Hucul
Achal Theke
Standardbred
PRE
Lusitano
#
#
Barb
n=1
HT1
n=2-5
HT2
n=5-10
HT3
n=10-20
HT4
n > 20
HT5
Arabian
HT6
Darley Arabian, 1700
Bartlets Childers, 1716
Flying Childers, 1714
Squirt, 1732
Blaze, 1733
Marske, 1750
Sampson, 1836
Eclipse, 1764
Young Marske,1771
Massenger, 1780
Pot8os, 1773
Mambrino, 1807
Waxy, 1790
King Fergus, 1775
Whalebone, 1807
Hambletonian 10, 1849
Rysdyk's Hambletonian
Camel, 1822
Sir Hercules, 1826
Harpham Turk, 1790
Defence, 1824
Vedette, 1854
Touchstone, 1831
Bird Catcher,1833
Perfectionist, 1899
Stockwell, 1849
Goldschaum,1891
The Duke, 1862
Phalaris, 1913
Gotthard,1949
Devils Own, 1887
Pharos, 1920
Hyperion, 1930
Rantzau,
1946
Cor de la Bryere, 1968
Ladykiller, 1961
Pasteur, 1963
Impressive, 1969
Nimmerdor, 1972
Detektiv, 1922
Northern Dancer, 1961
Standardbred
Welsh-A and B
HT2 (n=34)
Bavarian Warmblood, Austrian Warmblood, English thoroughbred, Hanoverian, Holstein,
Oldenburg, Quarter horse, Partbred Arabian, Riding pony, Rhinelander horse
Oldenburg
Trakehner
Warmblood
Dutch
Warmblood
HT3 (n = 59)
HT2 (n=9)
HT2 (n=1)
What can the Y-chromosomal haplotype distribution tell us
about the history of european horse breeds ?
v
v v
v
Deeper screen for y-chromosomal markers_JULY2015
Larger region - 1600 kb – more horses tested
- 43 horses from modern sport horse breeds – Thoroughred or Arabian influenced
Arabian
1
- 6 horses from autochthonous breeds
Baden-Württemberg
1
Icelandic horse
1
Bavarian warmblood
1
Mongolian Horse
1
Marwari horse
1
Pony from Jeju Island 1
French Montagne
1
Shetlandpony
2
Oldenburger
2
Sorraia
1
Haflinger
2
Holstein
2
Connemara Pony
2
Swiss warmblood
2
Trakehner
2
- 1 Przewalski horse
Westfalian
2
Thank you to my scientific collegues for sharing sequencing data
Hanoveran
3
Tosso Leeb
University of Bern
Stefan Rieder
Agroscope, Swiss National Stud Farm
Lipizzaner
3
Markus Neuditschko
Morgan Horse
5
Ottmar Distl
University of Veterinary Medicine Hannover
Julia Metzger
Qarter Horse
5
Ruedi Fries
TU Munich
Leif Andersson
Uppsala University
Southgerman Coldblood1
Gabriella Lindgren
Carl-Johan Rubin
Standardbred
7
Molly McCue
Jens Tetens
Georg Thaller
University of Minnesota
University Kiel
Modern horse Y-chromosomal Haplotype network_JULY2015
Modern horse Y-chromosomal Haplotype network_JULY2015
HT5
HT4
HT2
HT1
HTprz1
48 Individuals
58 mutations
28 Haplotypes
Age to ancestral node: 2000-2500 years
HT3
Modern horse Y-chromosomal Haplotype network_JULY2015
EXAMPLE 1: 40 Quarterhorse stallions
3 Haplotpyes detected
EXAMPLE 2: French Montage stallion lines
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French-Montagne is a Swiss heavy warmblood horse
- autochthonous mares - upgraded with stallions from GB,F and Sweden
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Illumina data from 21 stallions
New identification of breed specific Ychromosomal Haplotypes
Modern horse Y-chromosomal Haplotype network French Montagne
Vaillant
N-Linie
L-Linie
Doktryner
C-Linie
Summary
- Y-chromosomal markers provide a useful tool for the genetic
characterisation of stallion lines
- Describe population structures in a breed
- Forensic application
- The Y-chromosomal haplotype network serves as a backbone to
discriminate major modern horse clades
- Arabian, Spanish, Thoroughbreds
- The Y-chromosomal data clearly show the enormous influence of
Thoroughbred stallions on all sport horse breeds
- We offer stallion line characterisation based on this network at our
institute
Perspective
We are actively working on a further refinement of the network –
and are open for collaborations.
Thank you
Institute of Animal Breeding and
Genetics, Vetmeduni Vienna
Doris Rigler
Claus Vogl
Thomas Druml
Mathias Müller
Gottfried Brem
Institute of Population Genetics
Vetmeduni Vienna
Nicola Palmieri
Marlies Dolezal
Karin Schlangen
Christian Schlötterer
Max Dobretsberger, Bundesgestüt Piber
Thank you for NGS data
Tosso Leeb
Stefan Rieder
Markus Neuditschko
Ottmar Distl
Julia Metzger
Ruedi Fries
Leif Andersson
Gabriella Lindgren
Carl-Johan Rubin
Molly McCue
Jens Tetens
Georg Thaller
University of Bern
Agroscope, Swiss National Stud Farm
University of Veterinary Medicine Hannover
TU Munich
Uppsala University
University of Minnesota
University Kiel
Origin of the English Thoroughbred
Identification of Genetic Variation on the Horse Y Chromosome
Geographical distribution of domestic horse founders
v
v
n=1
n=2-5
n=5-10
n=10-25
n=25-50
v
v
n>50
Günderhengste des Englischen Vollblutes
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Englisches Vollblut, intensiver Einsatz zur Veredelung der Warmblutrassen
Geschlossenes Stutbuch seit 1791
Alle heute lebenden Englischen Vollblüter gehen zurück auf einen von 3
Gründerhengsten, die im 17. bzw. 18. Jahrhundert nach England importiert
wurden
BYERLEY TURK (*1684)
brown horse with strong oriental or Arabian features
GODOLPHIN ARABIAN (*1724)
Arabian horse or a Barb
DARLEY ARABIAN (about 1700) Arabian bought in Syria
the most important sire in the history of the English Thoroughbred - responsible for 95 % paternal lineages