TABLE 3.
Quantitative trait loci (QTL) for chlorophyll content detected in the DH118 × Jinmai 919 RIL population grown under different water regimes
| QTL name | Environment | Chr | LOD | R2 (%) | Add | Left marker | Right marker | Genetic interval (cM) | Physical interval (Mb) |
|---|---|---|---|---|---|---|---|---|---|
| Qchl.saw-1B | E1 | 1B | 2.58 | 6.34 | 0.61 | wsnp_Ex_c27176_36393952 | Kukri_c25512_53 | 417.616–434.069 | 640.848/648.454 |
| Qchl.saw-2A.1 | E5 | 2A | 3.42 | 5.90 | −0.56 | CAP11_s9154_121 | BS00100472_51 | 186.071–187.965 | 369.833/343.887 |
| Qchl.saw-2A.2 | E3 | 2A | 5.13 | 10.51 | −0.81 | Excalibur_c27023_134 | RFL_Contig3071_626 | 197.103–202.211 | 504.275/199.7962 |
| Qchl.saw-2B.1 | E5 | 2B | 2.65 | 4.67 | −0.50 | Ex_c19038_1581 | Tdurum_contig20262_440 | 43.902–47.744 | 19.394/18.932 |
| — | BLUP | 2B | 2.74 | 5.24 | −0.39 | Ex_c19038_1581 | Tdurum_contig20262_440 | 43.902–47.744 | 19.394/18.932 |
| Qchl.saw-2B.2 | E1 | 2B | 3.60 | 7.79 | −0.67 | Kukri_c34553_110 | RAC875_c98387_145 | 409.899–410.530 | 766.234/766.234 |
| Qchl.saw-2B.3 | E6 | 2B | 4.84 | 9.83 | −0.82 | RAC875_c19685_944 | Ku_c2936_1987 | 439.101–446.163 | 781.584/782.154 |
| Qchl.saw-2D.1 | E2 | 2D | 3.41 | 6.90 | 0.59 | wsnp_Ex_rep_c68555_67394261 | BS00018028_51 | 6.997–12.707 | 344.298/145.396 |
| Qchl.saw-2D.2 | BLUP—W | 2D | 4.35 | 9.60 | 0.50 | BS00018028_51 | Kukri_c22553_60 | 12.707–18.956 | 145.396/108.922 |
| Qchl.saw-2D.3 | E1 | 2D | 2.65 | 6.35 | 0.61 | Kukri_c22553_60 | RAC875_c11911_431 | 18.956–23.578 | 108.922/110.666 |
| Qchl.saw-3A.1 | E6 | 3A | 3.08 | 5.63 | −0.64 | RAC875_c20134_535 | BobWhite_c37325_92 | 48.634–61.187 | 14.851/20.328 |
| Qchl.saw-3A.2 | E3 | 3A | 2.82 | 5.58 | 0.57 | BobWhite_s65081_93 | Ra_c5515_2469 | 171.493–173.675 | 510.690/514.112 |
| Qchl.saw-3B.1 | E2 | 3B | 3.00 | 6.68 | −0.58 | wsnp_Ex_c16569_25082817 | Tdurum_contig31097_254 | 21.883–28.083 | 817.822/811.448 |
| Qchl.saw-3B.2 | E1 | 3B | 3.68 | 8.19 | 0.70 | BS00010818_51 | Excalibur_c8284_580 | 164.650–170.772 | 52.832/54.756 |
| — | E3 | 3B | 5.17 | 10.59 | 0.80 | BS00010818_51 | Excalibur_c8284_580 | 164.650–170.772 | 52.832/54.756 |
| — | BLUP—W | 3B | 5.38 | 11.43 | 0.56 | BS00010818_51 | Excalibur_c8284_580 | 164.650–170.772 | 52.832/54.756 |
| Qchl.saw-4B.1 | E4 | 4B | 3.08 | 5.76 | 0.57 | Excalibur_c17607_542 | RAC875_c15872_141 | 180.255–199.003 | 311.352/140.898 |
| Qchl.saw-4B.2 | E5 | 4B | 4.13 | 7.94 | 0.63 | wsnp_Ex_c3119_5763762 | wsnp_JD_c1549_2185341 | 171.195–180.754 | 443.454/363.305 |
| Qchl.saw-4B.3 | BLUP—D | 4B | 5.26 | 11.33 | 0.56 | RAC875_c48283_1574 | wsnp_Ex_c30695_39579408 | 195.003–216.053 | 140.898/20.589 |
| Qchl.saw-5A.1 | E4 | 5A | 3.23 | 6.24 | 0.84 | RAC875_rep_c109716_67 | IACX448 | 20.398–21.319 | 586.597/588.377 |
| Qchl.saw-5A.2 | E5 | 5A | 2.79 | 5.33 | 0.71 | wsnp_Ra_c3414_6378271 | Kukri_c61046_510 | 23.831–26.668 | 582.387/569.547 |
| — | BLUP—D | 5A | 3.11 | 5.28 | 0.53 | wsnp_Ra_c3414_6378271 | Kukri_c61046_510 | 23.831–26.668 | 582.387/569.547 |
| — | BLUP | 5A | 5.44 | 10.76 | 0.77 | wsnp_Ra_c3414_6378271 | Kukri_c61046_510 | 23.831–26.668 | 582.387/569.547 |
| Qchl.saw-5A.3 | E2 | 5A | 2.89 | 6.04 | −0.55 | GENE-2735_151 | RAC875_c79540_228 | 52.132–57.368 | 586.598/615.305 |
| — | E4 | 5A | 7.58 | 15.62 | −1.33 | GENE-2735_151 | RAC875_c79540_228 | 52.132–57.368 | 586.598/615.305 |
| — | E5 | 5A | 6.06 | 12.62 | −1.05 | GENE-2735_151 | RAC875_c79540_228 | 52.132–57.368 | 586.598/615.305 |
| — | E6 | 5A | 7.26 | 14.10 | −1.01 | GENE-2735_151 | RAC875_c79540_228 | 52.132–57.368 | 586.598/615.305 |
| — | BLUP—D | 5A | 9.73 | 18.36 | −0.95 | GENE-2735_151 | RAC875_c79540_228 | 52.132–57.368 | 586.598/615.305 |
| — | BLUP | 5A | 10.70 | 23.25 | −1.09 | GENE-2735_151 | RAC875_c79540_228 | 52.132–57.368 | 586.598/615.305 |
| Qchl.saw-5A.4 | E5 | 5A | 2.84 | 4.94 | −0.54 | wsnp_Ku_c7890_13514597 | wsnp_Ex_c9842_16228523 | 264.126–268.370 | 19.231/15.850 |
| Qchl.saw-5B.1 | E4 | 5B | 4.22 | 8.28 | 0.67 | Excalibur_c5594_1051 | BS00013829_51 | 292.392–294.925 | 520.8872/526.397 |
| Qchl.saw-5B.2 | E5 | 5B | 4.33 | 8.32 | 0.65 | RAC875_c32611_347 | BS00093591_51 | 320.986–322.563 | 536.681/536.052 |
| — | BLUP | 5B | 3.77 | 7.45 | 0.46 | RAC875_c32611_347 | BS00093591_51 | 320.986–322.563 | 536.6813/536.052 |
| — | BLUP—D | 5B | 6.86 | 12.15 | 0.59 | RAC875_c32611_347 | BS00093591_51 | 320.986–322.563 | 536.681/536.052 |
| Qchl.saw-6B.1 | E2 | 6B | 3.36 | 7.62 | 0.62 | BS00064027_51 | RFL_Contig2206_1694 | 129.185–138.393 | 680.937/690.730 |
| Qchl.saw-6B.2 | E3 | 6B | 4.76 | 9.70 | 0.76 | Tdurum_contig61383_627 | Tdurum_contig42301_1583 | 0.000–1.900 | 39.198/35.367 |
| Qchl.saw-7A.1 | E4 | 7A | 3.21 | 6.21 | 0.60 | wsnp_Ex_c40247_47349166 | BS00047691_51 | 13.785–15.675 | 116.113/118.327 |
| Qchl.saw-7A.2 | BLUP—D | 7A | 5.07 | 8.74 | 0.51 | RAC875_c62204_772 | BS00059928_51 | 32.704–36.455 | 615.341/603.092 |
| — | BLUP | 7A | 4.02 | 7.68 | 0.47 | RAC875_c62204_772 | BS00059928_51 | 32.704–36.455 | 615.341/603.092 |
| Qchl.saw-7A.3 | E5 | 7A | 3.28 | 6.17 | 0.56 | CAP7_c4608_228 | BS00105558_51 | 65.630–71.807 | 540.857/587.912 |
| Qchl.saw-7A.4 | E6 | 7A | 6.39 | 11.79 | 0.93 | BobWhite_c30461_131 | Excalibur_c22219_254 | 74.905–80.888 | 647.934/659.374 |
| Qchl.saw-7B.1 | E4 | 7B | 2.99 | 5.77 | 0.60 | RAC875_rep_c81362_198 | Excalibur_c29607_442 | 81.331–82.605 | 231.32/244.279 |