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Table 3 QTL detected for salt tolerance-related traits viz. overall phenotypic performance (SES), survival, physiological and agronomic traits during seedling stage based on single-marker analysis (SMA), interval mapping (IM) and composite interval mapping (CIM) in the Capsule/BR29 F2:3 population

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

Traits QTL Chr. Peak marker Position (cM) QTL bordering marker Additive effect aDirection of Phenotypic effect SMA, IM or CIM LOD Threshold LOD values at α0.05 and α0.01 after 1000 iterations in permutation analysis PVE (R2)
Agronomic traits
 SES qSES3.1 3 RM6329 111.0 RM5626- R3M53 1.1 BR29 SMA 5.3   23.0
3 RM6329 111.0 RM5626- R3M53 1.1 BR29 IM 5.3   23.0
3 RM6329 111.0 RM5626- R3M53 1.1 BR29 CIM 4.8 4.0–5.07 21.0
qSES5.2 5 RM3870 88.0 RM163-RM19199 1.2 BR29 SMA 3.7   17.0
5 RM3870 88.0 RM163-RM19199 1.9 BR29 IM 3.7   17.0
5 RM3870 88.0 RM163-RM19199 1.2 BR29 CIM 3.7   17.0
qSES12.3 12 RM252B 31.0 RM27615-RM27877 1.0 BR29 SMA 2.9   17.0
 Survival (%) qSur1.1 1 RM12208 162.9 RM472-RM14 −10.6 Capsule SMA 3.5   16.0
1 RM12208 162.9 RM472-RM14 −10.6 Capsule IM 3.9   18.0
1 RM12208 162.9 RM472-RM14 −10.6 Capsule CIM 4.0   17.0
qSur3.2 3 RM6329 111.0 RM5626- R3M53 −20.1 Capsule SMA 3.7   17.0
3 RM6329 111.0 RM5626- R3M53 −20.1 Capsule IM 3.7   18.0
3 RM6329 111.0 RM5626- R3M53 −20.1 Capsule CIM 3.7 3.7–4.9 18.0
qSur12.3 12 R12M27 67.1 S12055-RM28466 −12.0 Capsule SMA 2.8   14.0
12 R12M27 67.1 S12055-RM28466 −12.5 Capsule IM 3.1   16.0
 Shoot length qSL1.1 1 RM490 25.9 RM428A-AP3206f −6.2 Capsule SMA 3.4   16.0
qSL1.2 1 RM12208 162.9 RM472-RM14 12.0 BR29 IM 3.2   15.0
1 RM12208 162.9 RM472-RM14 10.0 BR29 CIM 3.0   14.2
qSL5.3 5 RM3870 88.0 RM163-RM19199 −3.69 Capsule SMA 3.9   18.0
5 RM3870 88.0 RM163-RM19199 −3.69 Capsule IM 4.5   20.0
5 RM3870 88.0 RM163-RM19199 −4.50 Capsule CIM 4.4 3.81–5.2 20.0
 Biomass-shoot qBMs3.1 3 RM6329 111.0 RM5626- R3M53 − 261.0 Capsule SMA 3.0   13.0
3 RM6329 111.0 RM5626- R3M53 −261.0 Capsule IM 3.0   13.0
3 RM6329 111.0 RM5626- R3M53 −261.0 Capsule CIM 3.0   13.0
qBMs5.2 5 RM3870 88.0 RM163-RM19199 −32.1 Capsule SMA 4.1   18.0
5 RM3870 88.0 RM163-RM19199 520.0 BR29 IM 4.2   19.0
5 RM3870 88.0 RM163-RM19199 500.0 BR29 CIM 3.8   17.0
qBMs12.3 12 RM252B 31.0 RM27615-RM27877 410.0 BR29 SMA 3.8   16.0
12 RM252B 31.0 RM27615-RM27877 410.0 BR29 IM 3.4   16.0
 Biomass-root qBMr1.1 1 RM12208 162.9 RM472-RM14 48.0 BR29 SMA 3.5   17.0
1 RM12208 162.9 RM472-RM14 42.0 BR29 IM 4.4   20.0
1 RM12208 162.9 RM472-RM14 70.0 BR29 CIM 4.4   16.0
qBMr3.2 3 RM6329 111.0 RM5626- R3M53 −31.0 Capsule SMA 3.6   17.0
3 RM6329 111.0 RM5626- R3M53 −42.0 Capsule IM 3.5   16.0
3 RM6329 111.0 RM5626- R3M53 −60.0 Capsule CIM 3.5   15.0
qBMr12.3 12 RM252B 31.0 RM27615-RM27877 58.0 BR29 SMA 3.5   15.0
12 RM252B 31.0 RM27615-RM27877 90.0 BR29 IM 3.3   15.0
Physiological traits
 Na+ concentration qNa1.1 1 RM12208 162.9 RM472-RM14 −0.30 Capsule IM 3.0   12.0
qNa2.2 2 RM525 109.0 RM525-RM208 −0.20 Capsule SMA 3.2   15.0
2 RM525 109.0 RM525-RM208 −0.20 Capsule IM 3.2   14.0
qNa3.3 3 RM6329 111.0 RM5626-R3M53 0.12 BR29 SMA 4.7   21.0
3 RM6329 111.0 RM5626-R3M53 0.10 BR29 IM 4.4   20.0
3 RM6329 111.0 RM5626-R3M53 0.10 BR29 CIM 4.3 4.2–5.5 24.0
qNa5.4 5 RM3870 88.0 RM163-RM3809 0.25 BR29 IM 2.8   13.0
 K+ concentration qK1.1 1 RM12208 162.9 RM472-RM14 −0.10 Capsule SMA 4.6   30.0
1 RM12208 162.9 RM472-RM14 − 0.10 Capsule IM 4.5   26.0
1 RM12208 162.9 RM472-RM14 −0.10 Capsule CIM 4.5 4.1–5.7 25.0
qK3.2 3 RM6329 111.0 RM5626-R3M53 −0.10 Capsule SMA 4.5   20.0
3 RM6329 111.0 RM5626-R3M53 −0.10 Capsule IM 4.5   20.0
3 RM6329 111.0 RM5626-R3M53 −0.10 Capsule CIM 4.5   16.0
qK12.3 12 RM252B 31.0 RM27615-RM27877 −0.10 Capsule SMA 3.5   15.0
12 RM252B 31.0 RM27615-RM27877 −0.10 Capsule IM 3.1   17.0
12 RM252B 31.0 RM27615-RM27877 −0.10 Capsule CIM 5.9   15.0
 Na-K ratio qNaK-R1.1 1 RM12208 162.9 RM472-RM14 1.5 BR29 IM 3.1   15.0
1 RM12208 162.9 RM472-RM14 2.5 BR29 CIM 3.0   14.0
qNaK-R2.2 2 RM525 109.1 RM3628-RM208 −2.8 Capsule SMA 3.5   17.0
2 RM525 109.1 RM3628-RM208 −2.5 Capsule IM 4.5   16.0
2 RM525 109.1 RM3628-RM208 −2.5 Capsule CIM 3.6   17.0
qNaK-R3.3 3 RM6329 111.0 RM5626- R3M53 −1.8 Capsule SMA 4.4   22.0
3 RM6329 111.0 RM5626- R3M53 −2.3 Capsule IM 3.7   17.0
3 RM6329 111.0 RM5626- R3M53 −2.5 Capsule CIM 3.7   17.0
qNaK-R5.4 5 RM3870 88.0 RM163-RM19199 1.4 BR29 IM 3.1   15.0
5 RM3870 88.0 RM163-RM19199 1.3 BR29 CIM 3.2   15.0
 SPAD readings qSPAD10.1 10 R10M17 33.2 RM501C-RM5806 −5.3 Capsule IM 3.2   15.0
10 R10M17 33.2 RM501C-RM5806 −5.3 Capsule CIM 3.2   15.0
  1. aQGene calculates both LOD and additive effect and displays the LOD. If we select a signed statistic such as Add effect (additive effect), a second plot is drawn below the main chromosome-map plot (LOD curve). A positive-signed effect represents an increasing allele from parent1, BR29; a negative-signed effect, an increasing allele from parent 2, Capsule (i.e. the favorable allele comes from Capsule)