Admixture in Horse Breeds Illustrated from Single Nucleotide Polymorphism Data
César Torres, Yaniv Brandvain
University of Minnesota, Department of Plant Biology, LSSURP Sciences Program
INTRODUCTION
RESULTS
More than 300 horse breeds exist in the modern world. Many of these
horse breeds are thought to have closely related evolutionary paths, but with
CONCLUSIONS
FIGURE 1: Treemix tree with multiple admixture arrows. Thoroughbred can
be seen involved in multiple admixture patterns.
FM
MON
the horse genome being sequenced recently (2007), genome-wide single
MINI
nucleotide polymorphism (SNP) studies confirming evolutionary relationships
NSWE
ICE
NORF
FIN
breeds that are thought to be evolutionary related by using the program
TUVA
NFST
Migration
weight
Treemix to create a phylogenic tree, which illustrates admixture in the multiple
0.5
SHET
horse breeds. Allele frequencies across 34,648 SNP sites formatted from the
genotype of 36 breeds (795 individuals in total) obtained with an Illumina
for the Swiss Warmblood.
CLYD
A very interesting result is that the Thoroughbred US seemed to
MNGP
when compared with the Quarter Horse. This implies that the
ARR
Beadchip, were used as the input data for the program.
10 s.e.
EXMR
yield a more negative f3 statistic value than the Thoroughbred UK
0
We found evidence for admixture events between several breeds of
confirmed by their negative f3 statistic values ranging as low as -0.0071
PRPF
PERU
LUST
AND
MOR
QH
PT
SB
AKTK
FLCR
CSP
MARM
HAN
FT
STBDNor
STBDUS
TB_UK
TB_US
SZWB
Thoroughbred US might have some admixture with the Quarter Horse.
Also both the Thoroughbred US and Thoroughbred UK were shown to
have admixture from each other.
horses, most of which were admixed with the Thoroughbred. Some horses were
In addition, no evidence was found of admixture in the
0.00
0.01
0.02
found to not have evidence of admixture. While for the Caspian, a breed
rediscovered in 1965, some admixture evidence was found, implying they might
0.03
Mangalarga Paulista, Exmoor, North Swedish Horse, Puerto Rican
Drift parameter
not be 100% pure Caspian. This was confirmed with F3 statistics tests (three
FIGURE 2: F3 statistic results for horses thought to have admixture from
the Thoroughbred.
population test). These findings will facilitate future studies of the origin of the
Admixture
among horse breeds
Admixture among horse breeds
0.05
domestic horse and its evolutionary path by providing new insights on each
breed and how they are related to each other. In the future we will use denser
frequencies.
•Out of the 50k SNP sites, only 34,648 were used due to triple allelic sites being
pure. As of the Caspian breed, few negative f3 statistic values were
found, illustrating traces of admixture. This is evidence for thinking
that the horses rediscovered might not be pure Caspian horses.
Quarter Horse ; Thoroughbred, _______
SZWB;
TB,__
Swiss
Warmblood ; Thoroughbred, _______
PT; TB,__
Paint Horse ; Thoroughbred, _______
HAN; TB,__
Hanoverian ; Thoroughbred, _______
Other
Other
QH; TB,__
FUTURE PLANS
0.03
•Since a higher number of SNP sites are needed to determine regions of
introgression, denser chips will be used.
0.02
•Denser chips will also allow to determine whether or not these sites are
are coding sequences.
•Linkage disequilibrium dating can be used to determine at what time
0.01
SNP Beadchip (DNA Microarray) were obtained and formatted into allele
o
o
o
o
o
Paso Fino, Arabian or Icelandic, implying that these breeds might be
the breeds’ history the admixture occurred.
0.00
•Samples of 36 horse breeds (795 individuals) genotyped on the Illumina 50k
admixture)
suggests
F3 valuef3(<0
value (<0
suggests admixture)
METHODS
0.04
chips to obtain more SNP sites allowing us to find regions of introgression and
determine whether or not they are coding sequences.
Swiss Warmblood, Paint Horse and Hanoverian; seem to have
admixture with the Thoroughbred from US and UK. This can be
PERC
BEL
FELL
SHR
are lacking. This project determines whether there is admixture between horse
A diverse number of horse breeds including the Quarter Horse,
removed.
•The program Treemix used the allele frequencies at the 34k SNP sites to infer
0
the patterns of population splits and admixture. The program uses the
5000
10000
15000
REFERENCES/
ACKNOWLEDGMENTS
20000
f3 rank
F3 Rank
similarities between allele frequencies to determine which horse breeds are
related to each other and if there is admixture between any of them illustrating
FIGURE 3: F3 statistic results for horses thought to have no admixture.
Putatively
pure
horse
breeds
Putatively
pure
horse
breeds
0.05
it with a red arrow. These trees were used to base our hypotheses.
0.04
•F3 statistic tests (also known as three population tests) were used to further
confirm if there was admixture between the horse breeds. This test compares
0.02
0.00
Admixture
from Breed 3
to Breed 2
-0.01
No admixture
0.01
F3
f3
statistic value implies admixture in individuals of the group A.
0.03
three populations or breeds in the form of (A; B, C), where a negative F3
MNGP
Breed 1
A
50% snps
B
50% snps
Breed 2 Breed 3
A
B
A
A
Breed 1
A
<50% snps
B
>50% snps
Breed 2 Breed 3
A
B
A
A
Breeds:
EXMR
NSWE
PRPF
breed
ARR
ICE
CSP
Pickrell and Pritchard (2012). Inference of population splits and mixtures
from genome-wide allele frequency data. PLoS Genetics. In Press.
Sponsored by NSF-REU in Molecular Genetics & Proteomics
Funded by UPR-PRISE Program NIH Grant #R25GM096955