S. No | Candidate gene | Nucleotide changea | Effect on protein sequence$ | Restriction sites | SIFT score | Allele designation | Germplasm accessions deconvolved through Sanger sequencing | |
---|---|---|---|---|---|---|---|---|
Gained in variant | Lost from reference | |||||||
Deleterious variants | ||||||||
1. | SSI | G3538A | G319S | BsrI, TatI | Cfr10I, HpaII | 0.00 | SSI-1 | Os-578, Os-631 |
2. | SSI | T4127C | Y420H | - | - | 0.00 | SSI-1 | Os-076, Os-468, Os-678 |
3. | SSIIa | G3761- | G592 fs | - | - | Frame shift | SSIIa-1 | Os-351 |
4. | SSIIa | G3797A | G604S | GsuI | HpaII | 0.00 | SSIIa-2 | Os-211, Os-468 |
5. | SSIIa | G4196A | V737M | NlaIII | Tsp4CI | 0.00 | SSIIa-3 | Os-363,Os-495 |
6. | SSIIIa | T3559A | V843E | TspDTI | 0.00 | SSIIIa-1 | Os-468, Os-495,Os-578 | |
Positive control | ||||||||
7. | SSI | G3538A | G319S | BsrI, TatI | Cfr10I, HpaII | 0.00 | SSI-1 | RSM 311 |
8. | SSIIa | G3797A | G604S | GsuI | HpaII | 0.00 | SSIIa-2 | RSM 271 |
9. | SSIIa | C978G | D283E | - | - | 0.00 | SSIIa-4 | RSM 311 |
10. | SSIIIa | C1615T | A195V | - | - | 0.00 | SSIIIa-2 | RSM 311, RSM 271 |
11. | SSIIIa | T3559A | V843E | - | TspDTI | 0.00 | SSIIIa-1 | RSM 311, RSM 271 |
12. | SSIIIa | C10761T | T1755I | - | - | 0.00 | SSIIIa-3 | RSM 311 |
Synonymous variants | ||||||||
1. | GBSSI | T1804C | P362= | BseYI | MaeI | 1.00 | No effect | Os-599 |
2. | SSI | T1449C | L181= | ApaI, BseSI, | - | 1.00 | No effect | Os-441 |
3. | SSI | T2252C | P229= | CauII, HpaII | EcoRII | 1.00 | No effect | Os-008 |
4. | SSI | C2288A | G241= | - | - | 1.00 | No effect | Os-048 |
5. | SSI | T2432A | I260= | - | Hpy178III,TspEI | 1.00 | No effect | Os-107 |
6. | SSI | G3937A | E388= | TspDTI | AluI, BseSI, CviJI, | 1.00 | No effect | Os-425 |
7. | SSIIa | T516C | D129= | FnuDII, HgaI, MaeIII, Tsp45I | SfaNI | 1.00 | No effect | Os-178 |
8. | SSIIa | T3901G | G638= | - | - | 1.00 | No effect | Os-433 |
9. | SSIIIa | T2276C | H415= | - | AvaIII, NlaIII | 1.00 | No effect | Os-058 |
10. | SSIIIa | C3135A | R702= | - | 1.00 | No effect | Os-100 | |
11. | SBEIa | C1569A | G304= | BciVI | CviJI | 1.00 | No effect | Os-717 |