Table 3.
QTLs detected on eight genotypic parameters of the model and on the first three axes of the PCA estimated on the RIL population.
| Trait | Sign. | LOD | Chr | Pos | Marker | CI cM (Mpb) | Nb genes | Mean Cer (sd) | Mean Lev (sd) | PVE | Coloc. (Albert et al., 2016)** |
|---|---|---|---|---|---|---|---|---|---|---|---|
| lp1* | 0.05 | 3.85 | 2 | 95.60 | TG167_Y02_52393366 | 89.73–107.19 (51.19 –54.79) | 480 | 0.01 | 0.01 | 13.75 | Nbfruits.C&WD |
| (0.00) | (0.00) | fw.C&WD FIR.WD | |||||||||
| FIR.WD dw.C SSC.Int | |||||||||||
| rxp* | 0.20 | 2.68 | 4 | 36.73 | Y04_03230589 | 33.63–52.44 | 192 | 0.17 (0.12) | 0.22 | 10.22 | ∅ |
| (0.30–0.48) | (0.12) | (0.13) | |||||||||
| lx1* | 0.10 | 2.81 | 4 | 61.27 | Y04_53862540 | 2.06–63.34 | 1604 | 0.001 | 0.002 | 10.7 | FIR.C and WD |
| (0.42–55.37) | (0.00) | (0.00) | |||||||||
| Axis3 | 0.20 | 2.46 | 4 | 86.96 | Y04_61146494 | 61.27–95.70 | 589 | −0.36 | 0.26 | 9.37 | Flw.C |
| (53.86–62.08) | 589 | (0.12) | (0.13) | ||||||||
| Flw.WD | |||||||||||
| Diam.C | |||||||||||
| fw.C | |||||||||||
| FIR.C&WD | |||||||||||
| dw.C | |||||||||||
| VitCFM.C&WD | |||||||||||
| Yield.C | |||||||||||
| nuM | 0.30 | 2.30 | 7 | 93.31 | Y07_67908188 | 82.11–93.31 | 408 | 0.05 | 0.03 | 8.80 | ∅ |
| (65.13–67.90) | (0.01) | (0.00) | |||||||||
| Axis2 | 0.20 | 2.49 | 7 | 88.00 | Y07_64327204 | 73.63–93.31 | 575 | 0.51 | −0.44 | 9.15 | ∅ |
| (63.64–67.90) | (0.20) | (0.19) | |||||||||
| lp | 0.05 | 3.31 | 8 | 42.12 | Y08_57208257 | 31.67–58.97 (54.32–59.92) | 479 | 0.22 (0.08) | 0.16 | 12.64 | pH.WD VitCFM.WD |
| (0.06) | VitCDM.C&WD | ||||||||||
| lx* | 0.30 | 2.24 | 8 | 42.12 | Y08_57208257 | 31.67–101.95 (54.32–65.60) | 1180 | 0.51 (0.05) | 0.03 | 8.71 | Flw.WD |
| (0.01) | pH.WD VitCFM.WD | ||||||||||
| VitCDM.C&WD | |||||||||||
| Yield.Int |
Traits transformed to ensure a normal distribution, LOG10(lp1); 1/rxp; LOG10(lx1); LOG10(lx).
Nbfruits, plant fruit number; fw, fruit fresh weight; FIR, fruit firmness; dw, fruit dry matter weight; SSC, solid soluble content; Flw, flowering time; Diam, stem diameter; pH, fruit pH; VitCFM, vitamin C content in fruit on a fresh weight basis; VitCDM, vitamin C content in fruit on a dry weight basis; Yield, fruit fresh weight per plant; C, control; WD, water deficit; Int, interactive between watering regimes.
“Sign.” indicates the significance threshold at which the QTL was detected. LOD is the log-likelihood at that marker. The chromosome is indicated under “Chr” and the position of the QTL is expressed in Haldane cM under “Pos.” The most closely associated marker is indicated. CI indicates the genetic confidence interval in Haldane cM calculated by LOD decrease of one unit, and its physical equivalent (Mpb) on genome assembly 2.5 between brackets. The number of genes in the QTL interval (genome annotation 2.4) is indicated. The average value of the two parental alleles (Cer and Lev, with the standard deviation between brackets) and the percentage of phenotypic variation explained by the QTL (PVE) are displayed. Colocalizations with phenotypic QTLs detected in Albert et al. (2016) in the same RIL population are indicated. C, QTL specific to the control condition; D, QTL specific to the water deficit condition; C&WD, QTL detected under both condition; Int, QTL with effect changing intensity or direction according to the watering conditions.