Table 4.
Highly differentiated SNPs validated with Sanger sequencing
| Gene name | Position in zebra finch genome | Min reads/pool | DI 454 | DI Sanger S Sweden N Sweden/ S Sweden Lithuania |
|---|---|---|---|---|
|
RNF6* |
Chr1: 48,509,942 |
13 |
0.92 |
0.69/0.56 |
|
RB1* |
Chr1: 56,558,186 |
9 |
1.00 |
0.81/0.50 |
|
ESD* |
Chr1: 57,059,422 |
12 |
0.92 |
0.63/0.38 |
|
ESD* |
Chr1: 57,059,472 |
11 |
0.91 |
0.75/0.43 |
|
XPOT |
Chr1A: 32,952,256 |
10 |
0.94 |
0.19 |
|
ADCYAP1R1 |
Chr2: 3,348,189 |
8 |
0.92 |
0.00 |
|
RNMT |
Chr2:101,951,215 |
13 |
0.93 |
0.19 |
|
RNMT |
Chr2:101,951,219 |
12 |
0.92 |
0.13 |
|
BAI3 |
Chr3: 86,028,013 |
9 |
0.92 |
0.06 |
|
ENSTGUG00000005084* |
Chr5: 3,850,065 |
18 |
0.91 |
0.88/0.88 |
|
FADS3* |
Chr5: 6,375,371 |
30 |
0.95 |
0.88/0.94 |
|
FADS3* |
Chr5: 6,375,565 |
25 |
0.96 |
0.94/0.94 |
|
FADS3* |
Chr5: 6,375,583 |
22 |
0.96 |
0.75/0.69 |
| SORD | Chr10: 3,477,546 | 15 | 0.94 | 0.00 |
Of the 14 candidate SNPs identified by the transcriptome analyses, eight (*) showed high to moderate differentiation (DI > 0.6) between southern (N = 8) and northern Swedish samples (N = 8) when independently validated by Sanger sequencing. These eight SNPs also showed elevated DIs between southern Swedish and Lithuanian samples (N = 8). The SNP in ADCYAP1R1 could only be successfully genotyped in four southern and five northern Swedish samples in the validation set.