Table 1 The estimated heritability and genetic effects of all significant SNPs for the plant height (PH) and the heading date (HD) through three analysis strategies.

From: Dissection of genetic architecture of rice plant height and heading date by multiple-strategy-based association studies

Trait

QTS

Chr.

Allele

Strategy

Effect type

Effect size

−log10 (P)

h2 (%)

(%)

PH

rs25397447

1

A/G

GWA

a

2.61

10.74

8.91

45.63

rs2745731

3

G/A

GWA

a

3.03

14.19

11.99

rs36929057

3

G/A

GWA

a

2.50

9.96

8.21

rs8819284

6

A/T

GWA

a

1.88

5.89

4.62

rs14788399

7

A/T

GWA

a

−1.83

5.60

4.37

rs4468159

11

C/T

GWA

a

−2.40

9.19

7.53

rs37194796

3

C/T

QBA

a

2.85

10.36

9.89

37.22

rs9040677

6

T/A

QBA

a

2.34

7.23

6.69

rs9669459

6

T/C

QBA

a

2.24

6.65

6.10

rs14788399

7

A/T

QBA

a

−2.72

9.54

9.04

rs4468159

11

C/T

QBA

a

−2.12

6.06

5.50

rs24562025

1

G/A

GBA

a

2.20

6.55

5.72

40.19

rs10179007

6

C/G

GBA

a

3.01

11.59

10.63

rs7478190

8

G/T

GBA

a

2.31

7.15

6.29

rs489068

12

C/T

GBA

a

2.63

9.04

8.14

rs10809004

12

C/A

GBA

a

−2.83

10.35

9.41

HD

rs12807091

1

T/C

GWA

a

1.58

5.57

4.67

41.56

rs22665688

1

C/T

GWA

a

2.29

10.89

9.71

rs26023433

1

C/T

GWA

a

1.41

4.54

3.71

rs3033880

6

A/T

GWA

a

−2.49

12.78

11.53

rs17909546

10

A/G

GWA

a

2.53

13.2

11.94

rs14583697

1

G/A

QBA

a

2.28

13.94

9.53

55.95

rs4139855

4

T/C

QBA

a

2.22

13.26

9.03

rs2083119

5

C/T

QBA

a

−1.94

10.28

6.88

rs3070122

6

G/A

QBA

a

−2.51

16.73

11.55

rs14516781

7

A/T

QBA

a

2.02

11.09

7.46

rs13634598

10

G/A

QBA

a

1.78

8.75

5.78

rs17462383

10

T/C

QBA

a

1.77

8.66

5.72

rs22139712

1

G/A

GBA

a

1.91

7.64

7.08

37.53

rs32347548

4

T/C

GBA

a

1.66

5.95

5.36

rs3112796

6

G/A

GBA

a

−1.78

6.77

6.19

rs12634148

10

C/T

GBA

a

1.45

4.67

4.09

rs17909546

10

A/G

GBA

a

2.24

10.31

9.79

rs457324

12

C/T

GBA

a

1.61

5.60

5.02

  1. QTS = the detected significant SNPs associated with the PH and the HD; Chr. = chromosome; Allele = paternal allele/maternal allele; GWA = genome-wide association, QBA = QTL-based association, GBA = gene-based association; a = additive effect for paternal allele homozygotes (QQ, ZH9308), -a for maternal allele homozygotes (qq, XQZB); −log10 (P) = inverse of the base 10 logarithm of p-values for significance of genetic effects; h2 (%) = heritability in percentage due to the genetic component effect;  (%) = total heritability equal to summation of heritabilities of all individual QTSs.
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