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Table 4 Segregation of SSR and InDel markers that exhibited association with QTL for salinity tolerance in selected salt-tolerant and salt-sensitive classes in an F2 population of a cross between Capsule (tolerant) and BR29 (sensitive) genotypes. A negative sign of the allele frequency difference between the tolerant and sensitive classes (Pr-Ps) indicates allele-frequency changes in the opposite direction to the parental phenotype

From: Assessing trait contribution and mapping novel QTL for salinity tolerance using the Bangladeshi rice landrace Capsule

Genetic Marker

Tolerant class

Sensitive class

Difference

Confidence interval

>  95% i.e. (Pr-Ps) ≥ 2σp

R2p (%)

E/Ea

E/Cap

Cap

Pr b

E/E

E/Cap

Cap

Ps b

Pr-Ps

Standard error (σp)

Chromosome 1

 RM472

14

21

12

0.223

10

23

14

0.245

−0.021

0.0617

0.123

–

 RM12208

10

33

4

0.351

13

18

16

0.191

0.160*

0.0638

0.128

12.66

 RM14

3

33

11

0.351

15

17

15

0.181

0.170*

0.0632

0.126

15.05

Chromosome 2

 RM525

17

21

9

0.223

12

26

9

0.277

−0.053

0.0630

0.126

–

 RM208

17

20

10

0.213

9

21

17

0.223

−0.011

0.0602

0.120

–

Chromosome 3

 RM4730

 

25

 

0.266

 

38

 

0.404

−0.138*

0.0681

0.136

6.11

 RM5626

7

25

15

0.266

15

24

8

0.255

0.011

0.0640

0.128

–

 RM6329

5

32

10

0.340

20

19

8

0.202

0.138*

0.0641

0.128

9.13

 R3M53

15

21

11

0.223

10

33

4

0.351

−0.128*

0.0653

0.131

5.50

Chromosome 5

 RM3870

10

19

18

0.202

11

33

3

0.351

−0.149*

0.0643

0.129

7.49

 RM3809

13

23

11

0.245

10

26

11

0.277

−0.032

0.0640

0.128

–

 RM19199

19

17

11

0.181

14

20

13

0.213

−0.032

0.0579

0.116

–

Chromosome 10

 RM501C

10

26

11

0.277

16

23

8

0.245

0.032

0.0640

0.128

–

 R10M17

12

22

13

0.234

16

21

10

0.223

0.011

0.0613

0.123

–

 RM5806

11

26

10

0.277

12

28

7

0.298

−0.021

0.0660

0.132

–

Chromosome 12

 RM27615

20

22

5

0.234

12

27

8

0.287

−0.053

0.0639

0.128

–

 RM252B

20

23

4

0.245

2

36

9

0.383

−0.138*

0.0669

0.134

6.23

 RM27877

6

32

9

0.340

15

28

4

0.298

0.043

0.0679

0.136

–

 S12055

6

31

10

0.330

15

29

3

0.309

0.021

0.0680

0.136

–

 R12M27

10

33

4

0.351

5

27

15

0.287

0.064

0.0678

0.136

–

 RM28466

11

22

14

0.234

14

21

8

0.223

0.011

0.0613

0.123

–

  1. *Significant at P < 0.05
  2. aE/E = homozygous for BR29 alleles; E/Cap = heterozygous; bCapsule allele frequency among the tolerant (Pr) and sensitive progeny (Ps); R2p = phenotypic variation explained
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