Table 5.
Results of composite interval QTL mapping and QTL × environment interactions of traits in Brassica rapa RILS. The trait and treatment for which the QTL was detected, chromosomal position (in cM), 2-LOD support intervals (in cM), additive effect with respect to the IMB211 allele, and percent variance explained are listed. The closest marker for each QTL is listed, with markers named with physical positions of SNPs relative to the B. rapa genome version 1.5 (available at BRAD). QTL are organized by cM position of the QTL peak for each chromosome in accordance with their position in Fig. 2. The P-value of QTL that demonstrate significant QTL × E interactions (P < 0.05) across treatments are indicated
| Trait/treatment | Position in cM (2-LOD intervals) | Additive effect | % variance explained | Closest marker | P-value of QTL × E (P < 0.05) |
|---|---|---|---|---|---|
| Chromosome 1 | |||||
| g s-WW | 25.6 (22.5-26.4) | 0.010 | 7.7 | A01x7382304 | |
| A-WW | 25.6 (24.2-26.4) | 0.91 | 4.6 | A01x7382304 | |
| A-DR | 27.3 (26.4-29.6) | 1.58 | 11.8 | A01x8029418 | |
| belowground biomass-DR | 30.5 (29.3-31.3) | 0.082 | 15.8 | A01x8409488 | |
| leaf area-DR | 30.5 (26.9-34.2) | 0.67 | 6.8 | A01x8409488 | |
| root:shoot ratio-WW | 30.5 (28.9-35) | 0.0015 | 12.6 | A01x8409488 | |
| aboveground biomass-DR | 32.2 (31.3-35.3) | 2.12 | 13.6 | A01x8682528 | |
| belowground biomass-WW | 33.4 (33-36) | 0.122 | 13.8 | A01x9090747 | |
| g s -DR | 34.2 (33.4-35.1) | 0.022 | 19.2 | A01x9141005 | p = 0.0269 |
| aboveground biomass-WW | 42.8 (40.8-44.5) | 3.04 | 9.3 | A01x10838067 | |
| LMA-WW | 46.1 (44.6-46.5) | -2.08 | 18.7 | A01x14360906 | p = 0.039 |
| leaf area-WW | 89.7 (86.5-91.3) | 1.33 | 7.4 | A01x26133588 | |
| δ13C-DR | 89.7 (88.3-91.1) | 0.63 | 23.0 | A01x26133588 | |
| W g -DR | 90.5 (86.2-91.3) | 2.67 | 17.1 | A01x26378441 | |
| aboveground biomass-WW | 91.3 (90.2-92.1) | 3.18 | 10.9 | A01x26495518 | |
| Fv'/Fm'-WW | 91.3 (90.4-92.1) | 0.032 | 24.0 | A01x26495518 | |
| height-DR | 91.3 (89.6-92.1) | 2.56 | 9.6 | A01x26495518 | |
| A-WW | 91.3 (89.5-92.1) | 1.47 | 11.4 | A01x26495518 | |
| A-DR | 91.3 (89.3-92.1) | 1.53 | 10.6 | A01x26495518 | |
| fruit production-WW | 91.3 (90.1-92.1) | 13.0 | 39.1 | A01x26495518 | |
| Fv'/Fm'-DR | 91.6 (90.3-91.3) | 0.038 | 20.6 | A01x26495518 | |
| fruit production-DR | 92.1 (89.7-92.1) | 10.2 | 17.5 | A01x26649666 | p = 0.0464 |
| g s -WW | 92.1 (89.2-92.1) | 0.012 | 10.8 | A01x26649666 | |
| δ13C -WW | 92.1 (86.3-92.1) | 0.31 | 6.4 | A01x26649666 | |
| leaf area-DR | 92.1 (90.1-92.1) | 0.62 | 5.5 | A01x26649666 | |
| Chromosome 2 | |||||
| g s -DR | 18.6 (14.8-21.2) | -0.014 | 23.9 | A02x1600026 | |
| leaf area-DR | 64.9 (49.7-65.3) | 0.65 | 5.9 | A02x9399462 | |
| root:shoot ratio-WW | 65.3 (52.3-69) | 0.0012 | 8.3 | A02x9415100 | |
| g s -WW | 72.7 (71.9-77.3) | 0.009 | 6.0 | A02x11479009 | |
| belowground biomass-DR | 72.7 (72.3-74.4) | 0.048 | 5.0 | A02x11479009 | |
| belowground biomass-WW | 76.6 (72.3-78.7) | 0.122 | 12.2 | A02x12174045 | |
| aboveground biomass-WW | 76.9 (75.6-77.7) | 2.30 | 5 | A02x12745444 | |
| leaf area-WW | 77.3 (73.1-79) | 1.41 | 7.4 | A02x12927010 | |
| Chromosome 3 | |||||
| belowground biomass-WW | 2 (0-8.1) | 0.104 | 8.5 | A03x97360 | |
| aboveground biomass-WW | 4.5 (2.4-6.2) | 2.68 | 7.0 | A03x1233655 | P = 0.0336 |
| leaf area-WW | 4.5 (2.4-8.1) | 1.39 | 7.7 | A03x1233655 | |
| days to flowering-WW | 9.8 (8.2-14.5) | 0.55 | 8.5 | A03x1786910 | |
| height-WW | 30.8 (29.9-31.2) | 4.75 | 25.7 | A03x5439663 | |
| height-DR | 30.8 (29.9-31.2) | 2.98 | 14.8 | A03x5439663 | |
| root:shoot ratio-DR | 36.7 (32.6-37.9) | -0.0035 | 9.9 | A03x6224923 | |
| days to flowering-WW | 67.8 (67-72.8) | 0.52 | 9.2 | A03x12997092 | |
| A-WW | 68.2 (67.9-69.5) | -1.84 | 16.7 | A03x13128260 | |
| A-DR | 70.5 (66.6-72.7) | -1.29 | 6.5 | A03x13687552 | |
| height-WW | 70.5 (68.6-71.1) | -2.44 | 5.7 | A03x13687552 | |
| height-DR | 75.2 (74.4-78.1) | -1.94 | 6.0 | A03x14491869 | |
| days to flowering-DR | 75.2 (74.4-79.8) | 0.57 | 7.4 | A03x14491869 | |
| δ13C -WW | 76.5 (75.6-77) | -0.63 | 27 | A03x14585658 | |
| δ13C -DR | 76.5 (75.6-78.1) | -0.81 | 37.7 | A03x14585658 | |
| Fv'/Fm'-DR | 76.5 (75.6-77.9) | -0.036 | 22.7 | A03x14585658 | |
| Fv'/Fm'-WW | 76.9 (79.4-81) | -0.039 | 40.0 | A03x14767219 | |
| fruit production-DR | 76.9 (75-78) | -25.6 | 21.5 | A03x14767219 | |
| W g-WW | 76.9 (75.7-78.1) | -1.07 | 11.0 | A03x14767219 | |
| aboveground biomass-DR | 77.7 (75.6-83.9) | -1.94 | 10.5 | A03x14933805 | |
| leaf area-DR | 80.2 (74.9-81) | -0.64 | 4.8 | A03x15439617 | |
| belowground biomass-DR | 81 (77.7-83.5) | -0.056 | 8.1 | A03x15589868 | |
| leaf area-WW | 83.1 (81-86.4) | -1.24 | 6.6 | A03x15983737 | |
| aboveground biomass-WW | 86 (83.9-90.1) | -2.48 | 6.1 | A03x16388952 | |
| Fv'/Fm'-WW | 110.4 (107.4-112.7) | 0.022 | 7.6 | A03x21952964 | |
| δ13C -DR | 115.7 (112.8-116.1) | 0.31 | 4.3 | A03x23208268 | |
| belowground biomass-DR | 115.7 (113-120.3) | 0.046 | 3.8 | A03x23208268 | |
| Chromosome 4 | |||||
| root:shoot ratio-DR | 23.5 (22.3-26.8) | 0.0186 | 4.8 | A04x7829955 | |
| δ13C -WW | 39.2 (36.9-41.3) | -0.27 | 5.2 | A04x12883502 | |
| fruit production-DR | 50.8 (49.7-52.8) | 18.8 | 6.9 | A04x15025757 | |
| A-WW | 52.4 (49.6-56) | 1.03 | 5.7 | A04x15133897 | |
| Chromosome 5 | |||||
| W g-WW | 19.5 (19.1-28.6) | -1.5 | 12.1 | A05x2841024 | |
| δ13C-DR | 47.1 (33-47.9) | -0.37 | 5.8 | A05x18948334 | |
| root:shoot ratio-DR | 72 (65.6-72.4) | -0.0027 | 5.3 | A05x22970845 | |
| Chromosome 6 | |||||
| root:shoot ratio-WW | 35.2 (30.4-39) | 0.0011 | 7.8 | A06x11042216 | |
| height-DR | 42.7 (40.7-46.6) | 2.10 | 7.4 | A06x16894473 | |
| days to flowering-DR | 50.5 (48.1-52.1) | 0.48 | 5.6 | A06x19335038 | |
| g s -WW | 53.9 (51.4-57.1) | 0.013 | 12.8 | A06x20616311 | |
| δ13C -WW | 76.2 (72.9-78.7) | -0.27 | 5.0 | A06x22977608 | |
| Chromosome 7 | |||||
| g s-WW | 1.2 (0-3.3) | 0.010 | 7.6 | A07x385264 | |
| δ13C -DR | 16.6 (16-18.2) | -0.52 | 10.7 | A07x9046546 | |
| δ13C -WW | 16.9 (16.6-19) | -0.51 | 7.7 | A07x9118045 | |
| g s -DR | 20.7 (19.4-23.2) | 0.019 | 15.0 | A07x9827612 | |
| days to flowering-DR | 28.2 (22.4-29.9) | -0.49 | 6.3 | A07x11888127 | |
| δ13C-DR | 31.1 (30-32.8) | 0.41 | 6.5 | A07x12258663 | |
| Fv'/Fm'-WW | 31.1 (30.3-33.2) | 0.021 | 6.5 | A07x12258663 | |
| A-WW | 46.5 (43.7-46.9) | 0.96 | 4.8 | A07x16000246 | |
| root:shoot ratio-DR | 70 (68.8-71.7) | -0.0024 | 7.7 | A07x20416077 | |
| root:shoot ratio-WW | 75.8 (75-77.5) | -0.0019 | 9.7 | A07x22133032 | |
| LMA-WW | 75.8 (74.6-77.5) | -1.24 | 9.4 | A07x22133032 | |
| Chromosome 8 | |||||
| LMA-WW | 38.6 (35.3-39.8) | -1.17 | 8.9 | A08x16635085 | |
| δ13C-WW | 52.6 (51.4-54.3) | -0.23 | 3.8 | A08x18475462 | |
| Fv'/Fm'-DR | 55.5 (54.3-57.1) | -0.017 | 5.4 | A08x18740873 | |
| height-WW | 70.6 (63.6-75.5) | -2.13 | 5.0 | A08x19709873 | |
| Chromosome 9 | |||||
| leaf area-WW | 10 (4.6-10.4) | -0.95 | 3.9 | A09x1412906 | |
| days to flowering-WW | 27.6 (27.3-30.9) | -0.55 | 8.8 | A09x4597771 | |
| δ13C-WW | 64.3 (61.4-66.8) | -0.31 | 6.2 | A09x11485309 | |
| g s-WW | 66.4 (64.4-68.5) | 0.013 | 11.0 | A09x12890329 | |
| W g-WW | 67.2 (62.3-69.7) | -0.85 | 6.5 | A09x13903113 | |
| days to flowering-WW | 67.6 (65.2-69) | 0.49 | 6.0 | A09x14125759 | |
| aboveground biomass-DR | 68.9 (68-71.9) | 3.15 | 26.2 | A09x14496888 | |
| fruit production-DR | 69.3 (68.5-70.3) | 31.7 | 23.0 | A09x18372050 | p = 0.0267 |
| leaf area-DR | 69.3 (67.7-70.1) | 1.05 | 12.8 | A09x18372050 | p = 0.0493 |
| aboveground biomass-WW | 69.7 (68.6-70.1) | 4.08 | 12.5 | A09x18352859 | |
| belowground biomass-WW | 70.1 (68.9-72.9) | 0.117 | 10.0 | A09x17690478 | |
| leaf area-WW | 70.5 (69.1-71.9) | 2.24 | 18.3 | A09x17079326 | p = 0.0091 |
| belowground biomass-DR | 71.9 (69.7-74.1) | 0.077 | 11.4 | A09x20118570 | |
| fruit production-WW | 74.2 (72.6-75.1) | 44.4 | 16.2 | A09x22639439 | p = 0.0377 |
| height-WW | 82.8 (80.4-83.2) | 2.09 | 4.9 | A09x25757167 | |
| days to flowering-WW | 91.4 (90.4-94.1) | 0.62 | 12.5 | A09x29142734 | |
| A-WW | 111.8 (107.7-115.1) | 0.87 | 4.1 | A09x32285047 | |
| g s-WW | 116.4 (114.3-118) | 0.009 | 5.4 | A09x33224026 | |
| leaf area-WW | 130.7 (128.9-133.8) | 2.08 | 18.6 | A09x34452870 | p = 0.0075 |
| Chromosome 10 | |||||
| height-DR | 16.9 (12.8-20.3) | 1.75 | 4.7 | A10x1631569 | |
| height-WW | 17.8 (16.5-20.3) | 2.07 | 4.8 | A10x1623273 | |
| Fv'/Fm'-WW | 18.8 (16.1-20.3) | 0.014 | 4.5 | A10x1374109 | |
| Fv'/Fm'-DR | 28.3 (25.2-36.1) | 0.016 | 4.6 | A10x6937636 | |
| fruit production-DR | 32.3 (27.3-33.5) | 14.6 | 7.1 | A10x7207245 | |
| fruit production-WW | 48.3 (46.2-53) | 24.8 | 5.6 | A10x11176662 | p = 0.04 |
| days to flowering-WW | 58 (56.3-58.6) | 0.54 | 8.3 | A10x12382013 | |
| g s-DR | 60 (59.2-61.6) | -0.013 | 6.2 | A10x12574844 | |
| root:shoot ratio-DR | 74.1 (72.6-76.1) | 0.0024 | 7.4 | A10x13586998 | p = 0.0091 |
| height-DR | 79.9 (76.1-80.7) | -1.82 | 4.5 | A10x14153811 | |
Fv'/Fm' chlorophyll fluorescence in light, g s stomatal conductance, W g intrinsic water-use efficiency (A/g s), δ 13 C carbon isotope composition, LMA leaf mass per area