Table 3.
TaqMan genotyping of SNPs in the Grey region
| |
|
|
Polymorphism1 |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| ID | Breed | Grey | SNP0 | SNP1 | Dup | SNP2 | SNP3 | SNP4 | SNP5 | SNP6 | SNP7 |
| 231 |
Arabian |
g/g |
|
A |
- |
C |
G |
C |
|
A |
|
| 446 |
Thoroughbred |
g/g |
|
A |
- |
C |
G |
C |
|
A |
|
| 1107 |
New Forest Pony |
g/g |
|
A |
- |
C |
G |
C |
|
A |
|
| 1268 |
Icelandic |
g/g |
|
A |
- |
C |
G |
C |
|
A |
|
| 2857 |
Connemara |
g/g |
|
A |
- |
C |
G |
C |
|
A |
|
| 5772 |
Shetland |
g/g |
|
A |
- |
C |
G |
C |
|
A |
|
| S062 |
Lipizzaner |
g/g |
|
A |
- |
C |
G |
C |
|
A |
|
| 6605 |
Shetland |
g/g |
|
A |
- |
C |
G |
T/C |
A/G |
G/A |
A |
| 1270 |
Icelandic |
g/g |
|
A |
- |
C |
- |
T/C |
A/G |
G/A |
A |
| 435 |
Arabian |
g/g |
|
A |
- |
C/T* |
G |
C |
|
A |
|
| 456 |
Arabian: Anc |
g/g |
|
A |
- |
C/T |
G |
C |
|
A |
|
| 800 |
Arabian: Anc |
g/g |
|
A |
- |
C/T |
G |
C |
A |
A |
A |
| 6972 |
Welsh |
g/g |
|
A |
- |
C/T |
G |
C |
|
A |
|
| D011 |
Lipizzaner |
g/g |
|
A |
- |
C/T* |
G |
C |
|
A |
|
| S046 |
Lipizzaner |
g/g |
|
A |
- |
C/T |
G |
C |
|
A |
|
| 6942 |
New Forest Pony |
G/g |
|
A |
+/− |
C |
G |
C |
G |
A |
A |
| S057 |
Lipizzaner |
G/g |
|
A |
+/− |
C |
G |
C |
G |
A |
A |
| 899 |
Arabian |
G/g |
|
A |
+/− |
C |
A/G |
T/C |
A/G |
A or G/A |
A/T |
| 222 |
Arabian |
G/g |
|
A |
+/− |
C |
A/G |
T/C |
|
G/A |
|
| 5726 |
Connemara |
G/g |
|
A |
+/− |
C |
A/G |
T/C |
|
G/A |
|
| 6591 |
Connemara |
G/g |
|
A |
+/− |
C |
A/G |
T/C |
|
G/A |
|
| D081 |
Lipizzaner |
G/g |
|
A |
+/− |
C |
A/G |
T/C |
|
G/A |
|
| D076 |
Lipizzaner |
G/g |
|
A/G |
+/− |
C |
A/G |
T/C |
|
G/A |
|
| 213 |
Arabian |
G/g |
|
A |
+/− |
C/T |
A/G |
T/C |
|
G/A |
|
| D091 |
Lipizzaner |
G/g |
|
A |
+/− |
C/T |
A/G |
T/C |
|
G/A |
|
| D007 |
Lipizzaner |
G/g |
|
A/G |
+/− |
C/T |
A/G |
T/C |
|
G/A |
|
| D010 |
Lipizzaner |
G/g |
|
A/G |
+/− |
C/T* |
A/G |
T/C |
|
G/A |
|
| 678 |
Arabian |
G/g |
|
A |
+/− |
C/T |
G |
T/C |
|
G/A |
|
| D004 |
Lipizzaner |
G/g |
|
A |
+/− |
C/T |
G |
T/C |
|
G/A |
|
| 452 |
Thoroughbred |
G/g |
|
A |
+/− |
C |
G |
T/C |
|
G/A |
|
| 3156 |
Lipizzaner |
G/g |
|
A |
+/− |
C |
G |
T/C |
|
G/A |
|
| 6577 |
Welsh |
G/g |
|
A |
+/− |
C |
G |
T/C |
|
G/A |
|
| 6611 |
Shetland |
G/g |
|
A |
+/− |
C |
G |
T/C |
|
G/A |
|
| SP1 |
Connemara:Sp |
G/g |
|
A |
+/− |
C |
G |
T/C |
|
G/A |
|
| SP2 |
Connemara:Sp |
G/g |
|
A |
+/− |
C |
G |
T/C |
|
G/A |
|
| SP3 |
Connemara:Sp |
G/g |
|
A |
+/− |
C |
G |
T/C |
|
G/A |
|
| SP4 |
Connemara:Sp |
G/g |
|
- |
+/− |
C |
G |
T/C |
|
G/A |
|
| D192 |
Lipizzaner |
G/g |
|
A/G |
+/− |
C |
G |
T/C |
|
G/A |
|
| 1271 |
Icelandic |
G/g |
|
A |
+/− |
C |
G |
T |
A |
G |
A/T |
| P023 |
Lipizzaner |
G/g |
A/T |
A/G |
+/− |
C |
A/G |
T/C |
|
G/A |
|
| S065 |
Lipizzaner |
G/g |
A/T |
A/G |
+/− |
C |
- |
T/C |
|
G/A |
|
| P038 |
Lipizzaner |
G/g |
A/T |
A/G |
+/− |
C |
A/G |
T/C |
|
G/A |
|
| L034 |
Lipizzaner |
G/g |
A/T |
A/G |
+/− |
C |
A/G |
- |
|
G/A |
|
| P076 |
Lipizzaner |
G/g |
A/T |
A/G |
+/− |
C |
A/G |
T/C |
|
G/A |
|
| L040 |
Lipizzaner |
G/g |
A/T |
A/G |
+/− |
C/T |
A/G |
T/C |
|
G/A |
|
| L049 |
Lipizzaner |
G/g |
A/T |
A/G |
+/− |
C/T |
A/G |
T/C |
|
G/A |
|
| D007 |
Lipizzaner |
G/g |
A/T |
A/G |
+/− |
C/T |
A/G |
T/C |
|
G/A |
|
| 230 |
Arabian |
G/G |
|
A |
+/+ |
C |
A |
T |
|
G |
|
| L010 |
Lipizzaner |
G/G |
|
A |
+/+ |
C |
A |
T |
|
G |
|
| D080 |
Lipizzaner |
G/G |
|
A/G |
+/+ |
C |
A |
T |
|
G |
|
| D006 |
Lipizzaner |
G/G |
|
G |
+/+ |
C |
A |
T |
|
G |
|
| 399 |
Arabian |
G/G |
|
A |
+/+ |
C/T |
A |
T |
|
G |
|
| 857 |
Arabian |
G/G |
|
A |
+/+ |
C/T* |
A |
T |
|
G |
|
| L004 |
Lipizzaner |
G/G |
|
A |
+/+ |
C/T |
A |
T |
|
G |
|
| D089 |
Lipizzaner |
G/G |
|
A/G |
+/+ |
C/T |
A |
T |
|
G |
|
| D098 |
Lipizzaner |
G/G |
|
G |
+/+ |
C/T |
A |
T |
|
G |
|
| 6210 |
Lipizzaner |
G/G |
|
A |
+/+ |
C |
A/G |
T |
|
G |
|
| D009 |
Lipizzaner |
G/G |
|
A/G |
+/+ |
C |
A/G |
T |
|
G |
|
| D079 |
Lipizzaner |
G/G |
|
A |
+/+ |
C/T |
A/G |
T |
|
G |
|
| P086 |
Lipizzaner |
G/G |
|
A |
+/+ |
C/T* |
A/G |
T |
|
G |
|
| D003 |
Lipizzaner |
G/G |
|
A/G |
+/+ |
C/T |
A/G |
T |
|
G |
|
| L053 |
Lipizzaner |
G/G |
|
A/G |
+/+ |
C/T* |
A/G |
T |
|
G |
|
| L024 |
Lipizzaner |
G/G |
|
A |
+/+ |
C |
G |
T |
|
G |
|
| 6580 |
Welsh |
G/G |
|
A |
+/+ |
C/T |
G |
T |
|
G |
|
| D102 |
Lipizzaner |
G/G |
|
A |
+/+ |
C/T |
G |
T |
|
G |
|
| L090 | Lipizzaner | G/G | A | +/+ | C/T* | G | T | G | |||
Results from TaqMan genotyping of selected SNPs located in the Grey region in 357 non-Grey and Grey horses from 8 different breeds, including the late-greying Connemara horses (Connemara:Sp) and Arabian horses (Arabian: Anc) carrying a non-Grey haplotype that is ancestral or closely related to the Grey haplotype. The table shows representative genotypes selected from all breeds. For SNP2, individuals with a strong signal for the variant T allele (C/T ratio equal 1) are marked with an asterisk. SNP0 SNP5 and SNP7 were genotyped by Sanger sequencing only in key individuals. SNP0 is at nucleotide position 6,553,858 in STX17.
1SNP1 is at nucleotide position 6,553,868 in STX17; Dup is the 4.6 kb duplication in STX17 causing Grey; SNP2 is at nucleotide position 6,587,140 in STX17; SNP3 is at nucleotide position 6,640,661 in TXNDC4; SNP4 is at nucleotide position 6,775,832 in INVS; SNP5 is at nucleotide position 6,778,924 in INVS; SNP6 is at nucleotide position 6,782,059 in INVS; SNP7 is at nucleotide position 6,790,986 in INVS.