Table A1  Results of composite interval QTL mapping and analyses of QTL × treatment interactions of physiological and phenological traits in B. rapa RILS
Trait treatmentPosition, cM (2-LOD intervals)LRAdditive effect% variance explainedClosest markerSignificant contrasts for QTL × E
Chromosome 1
Fv′/Fm0.01 (0.01–5.86)22.27−0.0210.42pW190aHN/A
A0.67 (0.01–4.04)18.95−0.848.17pW249dXN/A
Wg0.67 (0.01–13.89)20.65−1.729.56pW249dXN/A
E24.99 (24.6–48.6)16.140.176.09fito433N/A
gs38.25 (24.6–44.6)18.050.026.83fito019dN/A
Days to flowering-WL39.66 (24.99–50.77)14.47−1.345.16fito019d
LMA—CL41.66 (32.56–44.6)a+22.670.9410.43fito101a
LMA—CS43.22 (30.99–62.24)b+16.010.756.36pW108aE
Narea—CS48.6 (38.25–62.24)b+23.470.0588.92pX136bE
Narea—CL52.77 (38.25–62.24)a+27.460.07413.08pX136bE
Narea—WL52.77 (39.66–62.24)c19.240.0519.25pX136bE
A62.24 (50.6–71.28)c13.70.575.95fito222N/A
Chromosome 2
gs78.8 (67.3–85.28)d+17.97−0.016.37pW208aHN/A
E78.8 (66.01–96.89)d+13.69−0.165.27pW208aHN/A
Chromosome 3
Days to flowering—CL44.39 (31.83–55.73)e+21.59−1.910.89pW174cX
LMA—CL68.06 (55.73–79.83)f15.55−0.757.12pW147bH
LMA—WL66.06 (54.59–76.61)13.19−0.615.68pW147bH
Narea—CS68.06 (56.25–76.61)17.97−0.057.09fito492
Narea—CL82.49 (70.78–94.87)f16.72−0.056.58fito378a
E130.2 (122.97–142.21)16−0.186.61pW166aHN/A
Fv′/Fm149.03 (140.21–157.05)19.650.019.85fito019cN/A
gs130.2 (114.87–140.21)13.3−0.015.04pW166aHN/A
Chromosome 5
LMA—CS19.285 (5.185–26.825)13.450.785.28fito130b
Chromosome 6
gs108.37 (102.15–132.29)18.62−0.016.55fito041N/A
E108.37 (100.15–132.29)17.18−0.186.58fito041N/A
LMA—CS110.44 (72.54–132.29)12.08−0.644.65fito100a
### Fv′/Fm112.44 (90.15–120.29)11.550.015.57pX110aXN/A
Chromosome 7
Wg32.62 (26.62–42.96)g31.452.1115.26fito057N/A
Δ13C—CS33.4 (32.62–34.4)h+62.69−0.327.19fito057
Δ13C—WL33.4 (32.62–36.96)g38.75−0.2316.68fito057
Δ13C—CL42.96 (35.08–51.23)i+35.59−0.2413.52fito348
gs49.23 (32.62–56.99)g20.91−0.019.64fito348N/A
E49.23 (33.79–56.99)g26.06−0.2513.52fito348N/A
Narea—CS76.23 (68.08–76.23)j13.17−0.054.98pW202aX
Δ13C—WL74.23 (62.99–84.82)13.16−0.135.05pX144aH
Δ13C—CL79.91 (70.08–84.82)21.83−0.167.5pX101cH
###Δ13C—CS86.82 (70.08–96.9)j12.08−0.134.55fito101b
Days to flowering—CS96.88 (88.82–96.9)j19.01−2.059.32pW150cHWL/CS* CL/CS**
Chromosome 8
Narea—WL27.063 (17.063–33.953)17.80.058.28pW138aX
Narea—CL27.063 (15.063–59.123)14.070.055.54pW138aX
Narea—CS46.463 (33.953–59.123)17.80.0711.10pW177aE
Δ13C—CS34.463 (27.063–58.463)19.630.187.41pW245aE
LMA—CS58.463 (33.953–59.123)14.360.716.18pW177aE
LMA—CL58.463 (33.953–59.123)13.430.726.47pW177aE
Chromosome 9
Days to flowering—WL46.331 (35.451–54.661)13.93−1.445.05fito100b
Δ13C—CS56.391 (47.931–71.261)k+19.34−0.167.05pX147gE
Δ13C—CL62.591 (59.161–71.261)30.1−0.211.3fito549
Δ13C—WL64.591 (50.201–71.261)17.32−0.157.29fito549
LMA—CS56.391 (50.201–71.261)k+21.54−0.868.56pX147gE
LMA—WL70.591 (62.591–76.941)30.13−0.9414.01pW130cX
LMA—CL72.381 (59.161–80.441)13.25−0.685.85BRMS016
Narea—CS70.591 (70.591–76.941)k+18.17−0.056.73pW130cX
A72.381 (61.471–76.941)17.57−0.67.77BRMS016N/A
gs85.441 (76.941–97.441)32.91−0.0212.79fito033bN/A
Chromosome 10
Narea—WL35.334 (24.824–46.124)l+16.92−0.057.40pW129dH
Narea—CS35.334 (35.334–46.124)m+13.96−0.055.02pW129dH
Narea—CL35.334 (26.834–44.274)n+25.98−0.0710.84pW129dH
Days to flowering—CL26.834 (12.824–44.984)n+15.36−1.557.3pW240aE
Days to flowering—WL45.544 (44.274–58.434)l+32.07−2.1312.49pW174aX
LMA—WL46.284 (35.334–54.584)l+15.51−0.686.57pW255aE
  • The trait and treatment for which the QTL was detected, chromosomal position (in centimorgans), 2-lod support intervals (in centimorgans), likelihood ratio (LR) test statistic, additive effect of the IMB211 allele, and closest marker for each QTL are listed. QTL are organized by cM position of the QTL peak for each chromosome in accordance with their position in Figure 2. Note that chromosomes 5, 8, 9, and 10 are presented in inverted north–south orientation relative to their orientation as described by Iniguez-Luy et al. (2009) in order to be consistent with the accepted orientation (i.e., that of Parkin et al. 2005). Superscript letters next to centimorgan positions indicate sets of QTL that colocalized within a treatment for which multitrait composite interval mapping identified a single, significant QTL, supporting a hypothesis of pleiotropy. Superscript plus symbols next to the letters indicate locations in which period QTL from the appropriate environment were included in multitrait composite interval mapping analyses and results identified a single, significant QTL. A, photosynthetic rate; Fv′/Fm′, chlorophyll fluorescence in light; gs, stomatal conductance; E, transpiration rate; Wg, intrinsic water-use efficiency (A/gs); Δ13C, carbon isotope discrimination; Narea, nitrogen concentration on a leaf area basis; LMA, leaf mass per area. Also listed are pairs of treatments between which significant QTL × treatment interactions were detected. N/A indicates traits that were sampled in only the WL treatment. (###) QTL significant at 0.075 level. *P < 0.1, **P < 0.05.