Horse (Equine) STRs

As with human DNA, genetic material obtained from horses contains short tandem repeat (STR) markers that are highly variable among individuals and thus useful in differentiating between animals. Below is a list of some of the horse STR loci described in the literature and used by the International Society of Animal Genetics (ISAG).

 

STR Loci

 

Horse STR information kindly provided by Leanne van de Goor (VHL): Locus name, chromosomal location, repeat structure and repeat sequence, original reference, primer sequences, and the true size ranges of the amplicons.

 

Locus

Chrom.

Location

Repeat

structure

Repeat

sequence

Original

reference

Primer sequences (Forward and Reverse)

Amplicon

length (bp)

AHT4

24q14

Compound

(AC)nAT(AC)n

Binns et al. (1995)

F: AACCGCCTGAGCAAGGAAGT

R: CCCAGAGAGTTTACCCT

144-164

AHT5

8

Simple

(GT)n

Binns et al. (1995)

F: ACGGACACATCCCTGCCTGC

R: GCAGGCTAAGGAGGCTCAGC

126-144

ASB2

15q21.3-q23

Simple

(GT)n

Breen et al. (1997)

F: CCACTAAGTGTCGTTTCAGAAGG

R: CACAACTGAGTTCTCTGATAGG

216-250

ASB17

2p14-p15

Simple

(AC)n

Breen et al. (1997)

F: ACCATTCAGGATCTCCACCG

R: GAGGGCGGTACCTTTGTACC

87-129

ASB23

3q22.1-q22.3

Simple and

Compound

(TG)n and

(TG)nTT(TG)4

Irvin et al. (1998)

 

F: GAGGGCAGCAGGTTGGGAAGG

R: ACATCCTGGTCAAATCACAGTCC

175-211

CA425

UCDEQ425

28q18

Simple

(GT)n

Eggleston-Stott et al. (1997)

F: AGCTGCCTCGTTAATTCA

R: CTCATGTCCGCTTGTCTC

226-246

HMS1

15

Simple

(TG)n

Guerin et al. (1994)

F: CATCACTCTTCATGTCTGCTTGG

R: TTGACATAAATGCTTATCCTATGGC

170-186

HMS2

10

Compound

(CA)n(TC)2

Guerin et al. (1994)

F: CTTGCAGTCGAATGTGTATTAAATG

R: ACGGTGGCAACTGCCAAGGAAG

222-248

HMS3

9

Compound

(TG)2(CA)2TC(CA)n and (TG)2(CA)2TC(CA)nGA(CA)5

Guerin et al. (1994)

F: CCATCCTCACTTTTTCACTTTGTT

R: CCAACTCTTTGTCACATAACAAGA

148-170

HMS6

4

Simple

(GT)n

Guerin et al. (1994)

F: GAAGCTGCCAGTATTCAACCATTG

R: CTCCATCTTGTGAAGTGTAACTCA

151-169

HMS7

1q25

Compound

(AC)2(CA)n

Guerin et al. (1994)

F: TGTTGTTGAAACATACCTTGACTGT

R: CAGGAAACTCATGTTGATACCATC

165-185

HTG4

9

Complex

(TG)nAT(AG)5AAG(GA)5 ACAG(AGGG)3

Ellegren et al. (1992)

F: CTATCTCAGTCTTGATTGCAGGAC

R: CTCCCTCCCTCCCTCTGTTCTC

127-139

HTG6

15q26-q27

Simple

(TG)n

Ellegren et al. (1992)

F: GTTCACTGAATGTCAAATTCTGCT

R: CCTGCTTGGAGGCTGTGATAAGAT

84-102

HTG7

4

Simple

(GT)n

Marklund et al. (1994)

F: CCTGAAGCAGAACATCCCTCCTTG

R: ATAAAGTGTCTGGGCAGAGCTGCT

118-128

HTG10

21

Simple and

Compound

(TG)n and

TATC(TG)n

Marklund et al. (1994)

F: TTTTTATTCTGATCTGTCACATTT

R: CAATTCCCGCCCCACCCCCGGCA

95-115

LEX3

Xq

Simple

(TG)n

Coogle et al (1996)

F: ACATCTAACCAGTGCTGAGACT

R: GAAGGAAAAAAAGGAGGAAGAC

142-164

VHL20

30

Simple

(TG)n

Van Haeringen et al. (1994)

F: CAAGTCCTCTTACTTGAAGACTAG

R: AACTCAGGGAGAATCTTCCTCAG

87-105

 

 

STR Kits

Finnzymes Diagnostics offers several equine STR typing kits: http://diagnostics.finnzymes.fi/equine_genotypes.html

 

Example Horse STR Electropherogram (kindly provided by Leanne van de Goor (VHL))

 

Allele Nomenclature (ISAG Size to Repeat Number Conversion)

 

Conversion of ISAG nomenclature to repeat-number nomenclature (ISAG, International Society for Animal Genetics).

 

 

ISAG

Repeat

number

AHT4

AHT5

ASB2

ASB17

ASB23

CA425

HMS1

HMS2

HMS3

HMS6

HMS7

HTG4

HTG6

HTG7

HTG10

LEX3

VHL20

9

 

 

B

 

 

 

 

 

 

 

 

 

 

 

 

 

 

10

 

 

C

 

 

 

 

 

 

 

 

 

 

 

 

 

 

11

 

 

 

D

 

 

 

 

 

 

 

 

 

 

 

 

 

12

 

 

 

 

D

F

 

 

 

 

 

 

G

 

 

 

 

13

 

 

F

F

 

G

 

 

 

K

G

 

 

 

 

F

I

14

 

H

G

G

 

H

I

 

 

L

 

 

I

 

 

G

J

15

 

I

 

H

G

I

J

H

 

M

 

 

J

K

 

H

K

16

 

J

I

I

H

J

K

I

 

N

J

 

K

 

H

I

L

17

 

K

J

J

I

K

L

J

 

O

K

 

 

M

I

J

M

18

 

L

K

K

J

L

M

K

 

P

L

 

M

N

J

K

N

19

 

M

L

L

K

M

N

L

 

Q

M

 

N

O

K

L

O

20

 

N

M

M

L

N

 

M

H

 

N

 

O

P

L

M

P

21

 

O

N

N

 

O

 

 

I

 

O

 

P

 

M

N

Q

22

 

 

O

O

 

P

Q

O

 

 

P

 

Q

 

N

O

R

23

 

Q

P

P

 

 

 

P

 

 

Q

 

 

 

O

P

 

24

 

 

Q

Q

P

 

 

Q

L

 

 

 

 

 

P

Q

 

25

H

 

R

R

Q

 

 

R

M

 

 

 

 

 

Q

 

 

26

I

 

S

S

R

 

 

S

N

 

 

 

 

 

R

 

 

27

J

 

 

T

S

 

 

 

O

 

 

 

 

 

S

 

 

28

K

 

 

 

T

 

 

U

P

 

 

 

 

 

T

 

 

29

L

 

 

V

U

 

 

 

Q

 

 

 

 

 

 

 

 

30

M

 

 

W

V

 

 

 

R

 

 

K

 

 

 

 

 

31

N

 

 

 

 

 

 

 

S

 

 

L

 

 

 

 

 

32

O

 

 

Y

 

 

 

 

 

 

 

M

 

 

 

 

 

33

P

 

 

 

 

 

 

 

 

 

 

N

 

 

 

 

 

34

Q

 

 

 

 

 

 

 

 

 

 

O

 

 

 

 

 

35

R

 

 

 

 

 

 

 

 

 

 

P

 

 

 

 

 

36

 

 

 

 

 

 

 

 

 

 

 

Q

 

 

 

 

 

 

 

Population Data

Sequence information and allele frequencies from 17 equine STR loci (kindly provided by Leanne van de Goor (VHL))

 

Publications:

Binns, M.M., et al. (1995). The identification of polymorphic microsatellite loci in the horse and their use in thoroughbred parentage testing. The British Veterinary Journal 151: 9-15.

 

Bowling, A.T., et al. (1997). Validation of microsatellite markers for routine horse parentage testing. Animal Genetics 28: 247-252.

 

Chen, J.W., et al. (2010). Identification of racehorse and sample contamination by novel 24-plex STR system. Forensic Science International: Genetics 4: 158-167.

 

Choi, S.K., et al. (2008). Genetic characterization and polymorphisms for parentage testing of the Jeju horse using 20 microsatellite loci. Journal of Veterinary Medical Science 70: 1111-1115.

 

Dimsoski, P. (2003) Development of a 17-plex microsatellite polymerase chain reaction kit for genotyping horses. Croatian Medical Journal 44: 332-335.

 

Gurney, S.M.R., et al. (2010). Developing equine mtDNA profiling for forensic application. International Journal of Legal Medicine 124: 617-622.

 

Marklund, S., et al. (1994). Parentage testing and linkage analysis in the horse using a set of highly polymorphic microsatellites. Animal Genetics 25: 19-23.

 

Tozaki, T., et al. (2001). Population study and validation of paternity testing for Thoroughbred horses by 15 microsatellite loci. Journal of Veterinary Medicine and Science 63: 1191-1197.

 

Van de Goor, L.H.P., et al. (2010). A proposal for standardization in forensic equine DNA typing: allele nomenclature for 17 equine-specific STR loci. Animal Genetics 41: 122-127.

 

Van de Goor, L.H.P., et al. (2011). Population studies of 17 equine STR for forensic and phylogenetic analysis. Animal Genetics 42: 627-633.

 

[Return to STRBase]

Last Updated: 11/17/2011