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Table 2 Deleterious and synonymous variants discovered in the candidate genes through EcoTILLING by sequencing

From: EcoTILLING by sequencing reveals polymorphisms in genes encoding starch synthases that are associated with low glycemic response in rice

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

  1. aThe letter on the left side of the numeral indicates the nucleotide of the wild type; letter on the right side of the numeral indicates the altered variant nucleotide; numeral indicates the base pair position of the nucleotide change with respect to the gene sequence; “-” indicates single base pair deletion
  2. $“=” indicates a synonymous; the numeral indicates the residual number of the amino acid based on the gene model; letter on the left of the numeral indicates wild type amino acid; letter on the right side of the numeral indicates the altered amino acid; “fs” indicates the frameshift in the amino acid sequence