Table 2.
Sequence validation of polymorphisms identified in NPH3 target
| Nucleotide changea | Bandb | Effect | Genotype | SIFTc | PARSESNPd |
|---|---|---|---|---|---|
| C1045S | + | A475G | Leite | 0.13 | 9.4 |
| G867 K | + | V416L | FHIA01 | 1.00 | |
| G860R | + | E413= | Leite, Pisang Kayu, Mbwazirume | ||
| T797 W | + | I392= | FHIA_01 | ||
| C701Y | + | T360= | FHIA-01 | ||
| A672 W | + | T351S | Pahang | 0.42 | 10.8 |
| G641Re | + | K340= | FHIA-01 | ||
| A640Re | + | K340R | FHIA-01 | 0.59 | −0.6 |
| T576Y | + | S319P | Calcutta4 | 0.30 | |
| G515 K | + | R298S | FHIA-01 | 0.03 | 11.2 |
| G494R | + | G291= | FHIA-01 | ||
| G418S | + | C266S | FHIA-01 | 0.41 | 6.4 |
| T377 W | + | P252= | FHIA-01 | ||
| NDb | + (245 bp) | NA | Calcutta4 | ||
| Total (14) | 14 | 16 |
aNucleotide position on PCR amplicon
bAll nucleotide changes identified by sequencing were first identified by Ecotilling as a band on the gel image. In one case a 245-bp band was identified on the Ecotilling gel for which a corresponding polymorphism could not be confirmed by sequencing
cA non-synonymous SNP is predicted to be damaging to the encoded protein if the SIFT score is <0.05 (bold)
dA non-synonymous SNP is predicted to be damaging to the encoded protein if the PARSESNP score is >10 (bold)
eAdjacent polymorphisms appear as a single band on the gel image