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.

Sundström et al.

Sundström et al. BMC Genomics 2012 13:365   doi:10.1186/1471-2164-13-365

Open Data