Table 1. List of nucleotide polymorphisms in candidate genes.
| Gene | Nucleotide polymorphisma | Ratiob | Variation of amino acidc | SIFTd |
|---|---|---|---|---|
| GhSus1At | A918G | 0.612 | No | |
| G1783C | 0.342 | No | ||
| A2940T | 0.338 | T678= | ||
| GhSus1Dt | T650C | 0.089 | No | |
| G751A | 0.089 | V153I | 0 | |
| G2709C | 0.107 | E601Q | 0.12 | |
| GhSus3At | T881A | 0.072 | No | |
| T1320C | 0.072 | No | ||
| G1327A | 0.072 | No | ||
| T2294C | 0.018 | L504S | 0 | |
| A2472C | 0.018 | No | ||
| GhSus4Dt | A1886T | 0.025 | No | |
| T2167C | 0.025 | E388= | ||
| GhSus5Dt | G491T | 0.029 | L108F | 1 |
| C2648G | 0.025 | P660A | 1 | |
| GhSus6At | G3143T | 0.159 | No | |
| C4655T | 0.209 | No | ||
| G4697A | 0.209 | W755= | ||
| G5005A | 0.209 | No | ||
| GhSus7Dt | T192C | 0.755 | T64= | |
| C404T | 0.755 | D109= | ||
| T407C | 0.755 | E110= | ||
| GhSus8Dt | C577T | 0.09 | No | |
| T1334C | 0.069 | G298= |
aThe first letter indicates bp at this site in TM-1 sequence, followed by the position of the SNP in the TM-1 sequence, and then the nucleotide that is the rare variant at this site.
bRatio was calculated by dividing the number of similar nucleotide changes identified on the EcoTILLING gel by 277 upland cotton accessions.
cThe first letter indicates the common amino acid at this site, followed by the position of the SNP within the predicated protein sequence and the amino acid change induced by the variant nucleotide polymorphism; “=” means no change in amino acid encoded by that codon (synonymous variation); “No” means that SNP was in intron.
dA non-synonymous SNP is predicted to be damaging to the encoded protein if the SIFT score is <0.05 (bold).