Table 3 Unique SNP/InDel and candidate genes for seed shattering in qSH4 QTL region.

From: Genome-wide discovery of DNA polymorphisms by whole genome sequencing differentiates weedy and cultivated rice

Gene #

SNP location

PSRR-1

Bengal/Nona Bokra

Type of mutation

Locus ID

Putative function

1

Chr4: 33665181

C

T

start gain

LOC_Os04g56480

Pelota

1

Chr4: 33666866

G

A

missense

LOC_Os04g56480

Pelota

2

Chr4: 33489119

A

G

missense

LOC_Os04g56170

SBP-box

2

Chr4: 33489148

C

A

missense

LOC_Os04g56170

SBP-box (TF, control of early flower development)

3

Chr4: 33634394

G

A

start gain

LOC_Os04g56405

Expressed protein (predominantly expressed in developing seeds and SAM)

3

Chr4: 33632704

T

A

missense

LOC_Os04g56405

Expressed protein

3

Chr4: 33633208

A

G

missense

LOC_Os04g56405

Expressed protein

3

Chr4: 33633367

A

G

missense

LOC_Os04g56405

Expressed protein

3

Chr4: 33633406

A

G

missense

LOC_Os04g56405

Expressed protein

3

Chr4: 33633746

A

G

missense

LOC_Os04g56405

Expressed protein

4

Chr4: 33659169

A

C

missense

LOC_Os04g56460

BTB/POZ domain (mediates homomeric dimerisation and in some instances heteromeric dimerization, expressed on later seed developmental stages)

5

Chr4: 33662010

A

G

missense

LOC_Os04g56470

Amino acid transporter (expressed in inflorescence),

6

Chr4: 34091958

A

C

missense

LOC_Os04g57230

RecX

7

Chr4: 34274774

T

C

missense

LOC_Os04g57600

Zinc-finger

8

Chr4: 34210040

T

C

splice site

LOC_Os04g57500

Phosphatidate cytidylyltransferase

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