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
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 | Â | 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 | Â | 17.0 | |
5 | RM3870 | 88.0 | RM163-RM19199 | 1.9 | BR29 | IM | 3.7 | Â | 17.0 | ||
5 | RM3870 | 88.0 | RM163-RM19199 | 1.2 | BR29 | CIM | 3.7 | Â | 17.0 | ||
qSES12.3 | 12 | RM252B | 31.0 | RM27615-RM27877 | 1.0 | BR29 | SMA | 2.9 | Â | 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 | Â | 15.0 | |
1 | RM12208 | 162.9 | RM472-RM14 | 10.0 | BR29 | CIM | 3.0 | Â | 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 | Â | 19.0 | ||
5 | RM3870 | 88.0 | RM163-RM19199 | 500.0 | BR29 | CIM | 3.8 | Â | 17.0 | ||
qBMs12.3 | 12 | RM252B | 31.0 | RM27615-RM27877 | 410.0 | BR29 | SMA | 3.8 | Â | 16.0 | |
12 | RM252B | 31.0 | RM27615-RM27877 | 410.0 | BR29 | IM | 3.4 | Â | 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 | Â | 20.0 | ||
1 | RM12208 | 162.9 | RM472-RM14 | 70.0 | BR29 | CIM | 4.4 | Â | 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 | Â | 15.0 | |
12 | RM252B | 31.0 | RM27615-RM27877 | 90.0 | BR29 | IM | 3.3 | Â | 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 | Â | 21.0 | |
3 | RM6329 | 111.0 | RM5626-R3M53 | 0.10 | BR29 | IM | 4.4 | Â | 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 | Â | 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 | Â | 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 | Â | 15.0 | |
5 | RM3870 | 88.0 | RM163-RM19199 | 1.3 | BR29 | CIM | 3.2 | Â | 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 | ||