Table 4.
Polymorphism in Cm-ACO-1 and Cm-eiF4-iso detected by SOLiD sequencing and EcoTILLING[59]
| Position in the scaffold1 | Position in the gene (from ATG) | SNP MAF | aa change | Effect on protein according to SIFT2 | Exon | Detected by SOLiD/EcoTILLING | Agrestis3 | Momord | Melo |
|---|---|---|---|---|---|---|---|---|---|
| Coding region of Cm-ACO-1, CM3.5_scaffold00022 | |||||||||
| 3015744 |
41 |
A/G |
D14G |
Tolerated (1.00/3.02) |
1 |
Yes/yes |
G:6,7,4 |
A:21 |
A:5,2,8,- |
| |
|
0.68 |
|
|
|
|
|
|
|
| 3015944 |
241 |
A/G |
L46L |
|
2 |
Yes/yes |
G:15,6,5 |
A:15 |
A:5,5,8,1 |
| |
|
0.54 |
|
|
|
|
|
G:1 |
G:1,0,1,0 |
| 3016016 |
313 |
T/G |
L70L |
|
2 |
Yes/yes |
G:0,3,2 |
T:12 |
T:8,2,11,6 |
| |
|
0.99 |
|
|
|
|
|
|
|
| 3016091 |
388 |
T/A |
L95L |
|
2 |
Yes/yes |
T:3,1,0 |
T:10 |
T:7,-,2,2 |
| |
|
0.80 |
|
|
|
|
A:0,0,6 |
|
|
| 3016304 |
601 |
C/A |
L131M |
Not tolerated |
3 |
Yes/yes |
C:8,4,6 |
C:12 |
C:9,4,20,5 |
| |
|
0.87 |
|
(0.03/3.02) |
|
|
|
A:10 |
|
| - |
747 |
C/T |
D179D |
|
3 |
No/yes |
|
|
|
| 3016920 |
1216 |
T/C |
V294A |
Tolerated |
4 |
Yes/no |
T:11,7,7 |
T:29 |
T:18,5,20,7 |
| |
|
0.97 |
|
(0.12/3.03) |
|
|
|
C:1 |
C:1,0,0,1 |
| Coding region of Cm-eiF(iso)4E, CM3.5_scaffold00057 | |||||||||
| - |
26 |
G/A |
G9D |
Not tolerated |
1 |
No/yes |
|
|
|
| |
|
|
|
(0.00/4.32)* |
|
|
|
|
|
| 1030561 |
41 |
C/T |
A14V |
Not tolerated |
1 |
Yes/yes |
G:2,3,3 |
G:3 |
G:5,1,5,1 |
| |
|
0.90 |
|
(0.00/4.32)* |
|
|
A:4,0,0 |
|
|
| 1030440 |
162 |
T/C |
L54L |
|
1 |
Yes/yes |
G:31,22,3 |
G:12 |
G:31,1,5,0 |
| |
|
0.70 |
|
|
|
|
T:0,1,0 |
T:1 |
T:3,3,21,7 |
| 1029938 |
664 |
C/T |
S112N |
Tolerated |
2 |
Yes/no |
C:66,33,26 |
C:25 |
C:0,15,55,19 |
| |
|
0.99 |
|
(0.56/3.11) |
|
|
T:2,0,0 |
|
T:4,0,1,0 |
| 1029710 |
892 |
A/G |
L153L |
|
3 |
Yes/no |
A:91,49,30 |
A:46 |
A:75,17,54,30 |
| |
|
0.99 |
|
|
|
|
G:1,0,0 |
|
G:1,1,0,0 |
| 1029697 |
905 |
C/T |
K158E |
Not tolerated |
3 |
Yes/no |
T:0,38,13 |
T:31 |
T:67,10,39,26 |
| |
|
0.99 |
|
(0.02/3.12) |
|
|
C:5,0,0 |
|
C:3,0,0,0 |
| 1028781 |
1810 |
C/T |
D178G |
Tolerated |
4 |
Yes/no |
T:0,23,17 |
T:17 |
T:57,17,27,26 |
| |
|
0.99 |
|
(0.65/3.12) |
|
|
C:7,0,0 |
|
C:1,0,2,0 |
| 1028629 |
1962 |
C/T |
K198K |
|
5 |
Yes/no |
T:33,24,26 |
T:34 |
T:34,4,35,17 |
| |
|
0.99 |
|
|
|
|
|
|
C:2,0,1,0 |
| 1028619 |
1972 |
C/T |
S202G |
Not tolerated |
5 |
Yes/no |
T:42,32,33 |
T:37 |
T:52,8,49,21 |
| 0.99 | (0.00/3.14) | C:2 | C:1,0,0,0 | ||||||
1 Position in the melon genome assembly v3.5 available at MELONOMICS [36].
2 The effect of mutations was analyzed with SIFT [64]. Prediction score and median sequence conservation, respectively, are indicated in brackets. * Low confidence in the prediction (few sequences represented at those positions).
3 Number of reads of each allele are indicated in each pool, (−) means that this nucleotide has not been sequenced in the corresponding pool, numbers are ordered according to pool number, agrestis (pools 1, 2 and 3), momord (pool 4), melo (pools 5, 6, 7, 8).