Barbara Wallner

Genetic characterisation of stallion lines using Y-

chromosomal markers

World Breeding Federation for Sport Horses

General Assembly and Seminar

October 18th-20th2015, in Vienna, Austria

Barbara WallnerInstitute of Animal Breeding and Genetics

University of Veterinary medicine, Vienna

Famous Influential stallions-indication from the pedigrees

Barbara Wallner

Introduction

Darley Arabian Byerley Turk Godolphin Barb Kuhailian Haifi Traveler Njal Hárekur frá Geitaskarði Siglavy Bagdady Prince of Thule

- In most modern horse breeds only a limited number of male lineages are preserved

- Particular founder stallions contributed excessively to today´s breeds

- The influential founders often derive from distant geographical regions

Arabian

Thoroughbred

Spanish horse

• 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

18th century - establishment of the classical

Lipizzan stallion lines

Tracing of Lipizzan stallion lines

Barbara Wallner

Introduction

Barbara Wallner

Goals:

Discriminate the founder stallions genetically

- to reveal insight into their origin

- to monitor the influence of certain stallion lines

..so far - information about the origin of influential founders relies only on written records.....

Barbara Wallner

Genome Horse64 Chromosomes

2,8 x 2 Gigabases

Barbara Wallner

♂

Mode of inheritance: Autosomal, Y and mtDNA Genome

♂ ♀

♂ ♀ ♂ ♀

Barbara Wallner

Common ancestor

PresentLine 1 Line 2 Line 3 Line 4

Past

Median joining network

Y-chrosomale Haplotypes cattleKatanen et al. 2009

Y2

Y1

Which Y-chromosomal haplotypes are present in a breed?

How are the Y-chromosomal haplotypes related?

Interpreting Y-chromosomal networks

Barbara Wallner

With Y-chromosmal markers we can:

• Describe population structures in a breed

- stallion mediated geneflow flow between breeds

- number of popular founders

- investigate the origin of the stallion lines and their relationship

• Forensic application

- 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

paternal

mtDNA and Y-chromosomal lineages in horses

maternal

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

Cieslak et al. 2010 PlosONE

Vila et al. 2001 Science

Achilli et al. 2012 PNAS

Lippold et al. 2012 BMC

„Maternal and paternal lines often display a totally different story, which is

clearly evident in the domestic horse.“

Lindgren et al., NatGen 2004

High throughput sequencing technology

Barbara Wallner

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

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

Sequence 186kb from the Y-chromosome

Screening for Y-chromosomal variants

Network of the Haplotypes identified in 17 domestic horses

and in the Przewalski horse

Icelandic horse

Norwegian Fjord Shetland pony

English Thoroughbred

HT2T->A

Muta onHT3

T->-

Puta vegeneconversion

A<-G

Muta on

Geneconversion966bpdele on

HTprz1

37SNPsand3051bpdele on

HT5

HT4 HT1

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

Geographical distribution of Y-haplotypes

Russian Arabian

Quarter horse

Pinto

Arabian

Lipizzan

Icelandic horse

Norwegian Fjord

Shetland pony

##

Standardbred

English Thoroughbred

n=1 n=2-5 n=5-10 n=10-20 n > 20

American breeds

HT1 HT2 HT3 HT4 HT5 HT6

A

Paint Horse

Hucul

Achal Theke

Welsh

Haflinger

Noric

Lusitano

PRE

Barb

Appaloosa

Shagya Arabian

Pot8os, 1773

Waxy, 1790

Darley Arabian, 1700

Flying Childers, 1714

Blaze, 1733

Sampson, 1836

Massenger, 1780

Mambrino, 1807

Hambletonian 10, 1849Rysdyk's Hambletonian

Bartlets Childers, 1716

Squirt, 1732

Marske, 1750

Eclipse, 1764Young Marske,1771

Harpham Turk, 1790

King Fergus, 1775

Vedette, 1854

Oldenburg

Trakehner

Warmblood

HT2 (n=9)

Sir Hercules, 1826

Bird Catcher,1833

Stockwell, 1849

Bavarian Warmblood, Austrian Warmblood, English thoroughbred, Hanoverian, Holstein,

Oldenburg, Quarter horse, Partbred Arabian, Riding pony, Rhinelander horse

HT3 (n = 59)

Camel, 1822

Standardbred

Welsh-A and B

HT2 (n=34)

Touchstone, 1831

Nimmerdor, 1972Cor de la Bryere, 1968

Detektiv, 1922 Ladykiller, 1961

The Duke, 1862

Devils Own, 1887

Rantzau, 1946

Pasteur, 1963

Goldschaum,1891

Gotthard,1949

Hyperion, 1930

Phalaris, 1913

Pharos, 1920

Northern Dancer, 1961

Impressive, 1969

Whalebone, 1807

Defence, 1824

Perfectionist, 1899

Dutch

Warmblood

HT2 (n=1)

vv

v

v

What can the Y-chromosomal haplotype distribution tell us

about the history of european horse breeds ?

Thank you to my scientific collegues for sharing sequencing data

Tosso Leeb University of Bern

Stefan Rieder Agroscope, Swiss National Stud Farm

Markus Neuditschko

Ottmar Distl University of Veterinary Medicine Hannover

Julia Metzger

Ruedi Fries TU Munich

Leif Andersson Uppsala University

Gabriella Lindgren

Carl-Johan Rubin

Molly McCue University of Minnesota

Jens Tetens University Kiel

Georg Thaller

Larger region - 1600 kb – more horses tested

- 43 horses from modern sport horse breeds – Thoroughred or Arabian influenced

Arabian 1

Baden-Württemberg 1

Bavarian warmblood 1

Marwari horse 1

French Montagne 1

Oldenburger 2

Haflinger 2

Holstein 2

Connemara Pony 2

Swiss warmblood 2

Trakehner 2

Westfalian 2

Hanoveran 3

Lipizzaner 3

Morgan Horse 5

Qarter Horse 5

Southgerman Coldblood1

Standardbred 7

Deeper screen for y-chromosomal markers_JULY2015

- 6 horses from autochthonous breeds

Icelandic horse 1

Mongolian Horse 1

Pony from Jeju Island 1

Shetlandpony 2

Sorraia 1

- 1 Przewalski horse

Modern horse Y-chromosomal Haplotype network_JULY2015

HT2 HT3

HTprz1

HT5

HT4 HT1

48 Individuals

58 mutations

28 Haplotypes

Age to ancestral node: 2000-2500 years

Modern horse Y-chromosomal Haplotype network_JULY2015

Modern horse Y-chromosomal Haplotype network_JULY2015

3 Haplotpyes detected

EXAMPLE 1: 40 Quarterhorse stallions

New identification of breed specific Y-

chromosomal Haplotypes

- French-Montagne is a Swiss heavy warmblood horse

- autochthonous mares - upgraded with stallions from GB,F and Sweden

- Illumina data from 21 stallions

EXAMPLE 2: French Montage stallion lines

Modern horse Y-chromosomal Haplotype network French Montagne

Vaillant

C-Linie

N-Linie

L-Linie

Doktryner

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.

Max Dobretsberger, Bundesgestüt Piber

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

Thank you

Thank you for NGS data

Tosso Leeb University of Bern

Stefan Rieder Agroscope, Swiss National Stud Farm

Markus Neuditschko

Ottmar Distl University of Veterinary Medicine Hannover

Julia Metzger

Ruedi Fries TU Munich

Leif Andersson Uppsala University

Gabriella Lindgren

Carl-Johan Rubin

Molly McCue University of Minnesota

Jens Tetens University Kiel

Georg Thaller

Origin of the English Thoroughbred

Geographical distribution of domestic horse founders

Identification of Genetic Variation on the Horse Y Chromosome

v

v

v

v

n=1 n=2-5 n=5-10 n=10-25 n=25-50 n>50

Günderhengste des Englischen Vollblutes

• 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