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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