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Table 4 Summary of association analyses between FGP of F 2:3 seeds and SSR genotypes on chromosome 5

From: Agronomic and genetic analysis of Suweon 542, a rice floury mutant line suitable for dry milling

Locusa

Mirror-map informationb

Segregation testc

Genotype meand

ANOVAe

Genetic effectf

Marker

Ap

Size (bp)

Mbp

BAC/PAC

cM

A

H

B

χ2

A

H

B

F

R 2

Add

Dom

DeD

RM5693

1

200

0.46

OSJNBa0068N01

4.6

18

59

17

5.4

44.4

34.2

23.6

1.6

    

RM3322

1

121

4.26

P0685E10

32.0

31

44

17

3.8

52.0

30.5

13.7

8.7

0.164

-19.2

-2.3

0.12

RM3193

2

126

4.97

P0453H11

36.4

29

48

17

2.6

56.3

29.3

10.4

13.6

0.231

-23.0

-4.1

0.18

RM5844

1

195

9.15

OSJNBa0032D15

53.5 ~ 54.3

30

40

24

2.4

66.3

25.7

8.1

39.3

0.463

-29.1

-11.5

0.39

RM3838

2

198

16.55

OSJNBa0077J17

60.7

28

39

26

2.0

63.0

26.3

15.4

21.5

0.323

-23.8

-12.9

0.54

RM6024

2

178

17.81

OJ1118_F06

67.5

25

41

27

1.1

75.6

26.0

7.1

70.8

0.612

-34.3

-15.3

0.45

RM18614

2

164

19.22

OSJNBa0014C03

73.9 ~ 75.0

22

51

21

0.5

81.9

27.0

1.8

101.7

0.691

-40.1

-14.9

0.37

RM164

2

265

19.26

OSJNBa0014C03

73.9 ~ 75.0

20

54

20

1.7

91.6

25.5

0.4

272.0

0.857

-45.6

-20.5

0.45

RM18620

3

245

19.28

OSJNBb0092G21

73.9 ~ 75.0

20

54

20

1.7

91.6

25.5

0.4

272.0

0.857

-45.6

-20.5

0.45

RM18624

3

304

19.33

OSJNBb0092G21

73.9 ~ 75.0

20

54

20

1.7

91.6

25.5

0.4

272.0

0.857

-45.6

-20.5

0.45

RM18639

3

317

19.73

OJ1174_H11

75.0 ~ 77.4

19

53

22

1.4

95.5

26.3

0.4

538.7

0.922

-47.6

-21.6

0.45

RM18648

3

296

19.86

P0040B10

75.0 ~ 77.4

18

53

23

1.7

95.2

27.6

1.7

290.8

0.865

-46.8

-20.9

0.45

RM1386

3

197

20.06

P0668F02

75.0 ~ 77.4

18

53

23

1.7

95.2

27.6

1.7

290.8

0.865

-46.8

-20.9

0.45

RM3351

1

134

20.76

OJ1212_B02

80.7

20

44

30

2.1

77.8

31.1

9.8

49.2

0.520

-34.0

-12.7

0.37

RM5558

2

173

21.25

OJ1301_G07

86.0

23

40

31

3.0

71.3

30.6

11.2

37.0

0.448

-30.1

-10.7

0.35

RM5642

2

129

22.25

OJ1126_D01

92.0

22

38

33

5.1

62.4

31.9

18.4

14.2

0.240

-22.0

-8.5

0.38

RM3870

2

193

22.96

OJ1387_F08

95.3

23

38

33

5.0

65.5

29.7

17.6

19.5

0.300

-24.0

-11.9

0.50

RM3476

1

132

23.91

OJ1004_E02

101.0

18

46

30

2.6

62.8

35.6

15.0

14.3

0.239

-23.9

-3.3

0.14

RM7653

2

121

27.42

OSJNBa0079H23

111.6

18

43

33

4.8

52.1

31.7

27.7

3.4

0.069

-12.2

-8.1

0.67

RM1054

1

150

29.23

OJ1007_H05

122.0

23

41

30

2.2

49.8

28.1

30.6

3.4

0.069

-9.6

-12.1

1.26

  1. aDNA markers were tested in 94 F2 progenies derived from Suweon 542/Milyang 23. After conducting a first round of association analyses over well-defined 6 anchor markers (application: Ap = 1), an additional 9 SSR markers (Ap = 2) were applied to narrow down the putative location responsible for the floury endosperm characteristics on chromosome 5. Five SSR markers (Ap = 3) were further applied to localize the flo7(t) nearby a BAC lone OJ1174_H11 (BenBank Acc. = AC104708.2), tagged by a SSR marker, RM18639.
  2. bThe expected PCR product size inferred by e-Landings on a reference rice genome, ‘Os-Nipponbare-Reference-IRGSP-1.0’ (http://rapdb.dna.affrc.go.jp/download/%irgsp1.html). The cM position was directly adopted from the IRGSP Build5 Pseudomolecules (http://rgp.dna.affrc.go.jp/E/%IRGSP/Build5/build5.html) according to the locations of BAC/PAC clones harboring priming sites for each SSR marker.
  3. cA and B are homozygous for Suweon 542 and Milyang 23 allele types, respectively, and H indicates heterozygous progenies at the tested locus. All χ2 values for the segregation distortion test were not significant at P < 0.05.
  4. dMean floury grains percentage (FGP) for each genotype category revealed by the SSR markers.
  5. eSingle-locus ANOVA to test associations between SSR marker genotypes and FGP. For the F-test, markers having less than 0.05 for significance were declared as significant empirically (*P < 0.05 and ***P < 0.001). The explainable variation portion of FGP at the tested locus (R2) is also shown.
  6. fAdditive effect (Add), dominance effect (Dom), and degree of dominance (DeD) were estimated for the significant loci: Add = (B mean – A mean) / 2, Dom = H mean – (B mean + A mean) / 2, and DeD = Dom / Add, where A and B are homozygous F2 individuals for Suweon 542 and Milyang 23 while H is heterozygous individuals at the tested locus.