Table 2 Summary of 13 possible functional SNPs within five known genes.

From: Genetic basis and network underlying synergistic roots and shoots biomass accumulation revealed by genome-wide association studies in rice

Trait

Signal under FarmCPU

Known gene

Non synonymous SNP in known gene

MAF

Alleles

Elite allele

− log(P) under GLM

Full population

Japonica

Indica

Root weight

Chr6_30045542

OsPTR9

Chr6_29839744

0.23

A/T

T

7.2

3.36

–

Chr6_29840728

0.24

A/C

C

6.67

4.19

–

Chr6_29840758

0.24

T/C

C

6.22

3.92

–

R/S

Chr6_30047965

OsPTR9

Chr6_29839744

0.23

A/T

T

8.82

4.11

–

Chr6_29840728

0.24

A/C

C

7.69

3.83

–

Chr6_29840758

0.24

T/C

C

7.36

3.74

–

Root length

Chr6_30077572

OsPTR9

Chr6_29839102

0.13

A/G

G

2.23

–

2.86

Chr7_1278547, Chr7_1244488

Crl-5, OsPR1a

Chr7_1303391

0.44

C/G

C

2.09

–

2.41

Root thickness

Chr4_29374382

GLR3.1

Chr4_29566027

0.38

A/C

A

2.63

–

2.2

Chr4_29567859

0.39

C/T

T

2.86

–

2.07

Chr4_29567998

0.38

A/G

G

3.02

–

2.23

Chr4_29569521

0.4

C/T

C

2.11

–

2.58

Shoot length

Chr1_24783550

OsWRKY11

Chr1_25011608

0.47

A/G

A

5.75

–

3.47

Chr6_21936682

d35

Chr6_22074153

0.36

G/C

G

6.54

3.28

–

Chr6_22074288

0.3

A/G

A

4.61

2.57

–

Chr6_22076053

0.36

A/G

G

6.5

2.91

–

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