Table 2.
Peak QTLs from the mapping of individual time points and growth curve parameter for Area, Height, Senescence and water use (WA).
| Trait | DAS | peak.SNP | SN | chr | cM | Alchemy | Brompton | Claire | Hereward | Rialto | Robigus | Soissons | Xi19 | h2 | logP | P-value | Lower | Upper |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Area | 136 | RAC875_rep_c105718_585 | Q1 | chr4D | 40.11 | 69244.19 | 70726.64 | 68961.25 | 71277.8 | 64324.87 | 88639.24 | 82420.8 | 68635.23 | 0.26 | 5.03 | 0 | 1100001 | 2100001 |
| Area | 148 | RAC875_rep_c105718_585 | Q1 | chr4D | 40.11 | 79011.69 | 80634.7 | 79132.84 | 79329.72 | 72228.77 | 104657.47 | 95155 | 78610.13 | 0.30 | 6.13 | 0 | 1100001 | 2200001 |
| Area | 158 | RAC875_rep_c105718_585 | Q1 | chr4D | 40.11 | 83601.38 | 84625.25 | 83505.17 | 82474.3 | 74737.2 | 110709.22 | 99681.57 | 81966.03 | 0.32 | 6.84 | 0 | 1100001 | 2300001 |
| Area | 166 | RAC875_rep_c105718_585 | Q1 | chr4D | 40.11 | 85421.27 | 86303.78 | 84829.58 | 85063.95 | 76910.64 | 115352.03 | 101544.8 | 84263.48 | 0.33 | 7.24 | 0 | 1100001 | 2300001 |
| Area | 170 | RAC875_rep_c105718_585 | Q1 | chr4D | 40.11 | 84679.14 | 86124.21 | 85332.53 | 84096.08 | 76355.65 | 114026.02 | 100925.26 | 84268.74 | 0.32 | 7.01 | 0 | 1100001 | 2200001 |
| Area | 180 | RAC875_rep_c105718_585 | Q1 | chr4D | 40.11 | 84520.25 | 83636.76 | 84650.83 | 83425.9 | 75116.47 | 113026.45 | 97528.08 | 81995.76 | 0.32 | 6.98 | 0 | 1100001 | 2300001 |
| Area | 189 | RAC875_rep_c105718_585 | Q1 | chr4D | 40.11 | 82732.5 | 82136.26 | 83503.19 | 81775.89 | 72993.25 | 111018.8 | 94719.31 | 81649.07 | 0.32 | 6.69 | 0 | 1100001 | 2300001 |
| Height | 104 | IAAV1650 | Q2 | chr5A | 227.15 | 359.21 | 351.54 | 372.03 | 365.19 | 366.47 | 370.33 | 365.25 | 483.14 | 0.38 | 8.5 | 0 | 62600001 | 78600001 |
| Height | 117 | Kukri_rep_c68594_530 | Q3 | chr4D | 24.93 | 549.21 | 552.46 | 547.53 | 529.87 | 546.62 | 605.29 | 602.12 | 538.92 | 0.32 | 6.9 | 0 | 1000001 | 2100001 |
| Height | 117 | Tdurum_contig42083_1539 | Q7 | chr4D | 3.09 | 560.86 | 577.26 | 562.7 | 546.19 | 547.5 | 582.53 | 573.2 | 580.93 | 0.28 | 5.52 | 0 | 100001 | 200001 |
| Height | 121 | RAC875_c1673_193 | Q4 | chr4D | 32.24 | 587.3 | 595.07 | 586.07 | 585.94 | 586.81 | 656.97 | 665.65 | 574.99 | 0.25 | 4.71 | 0.01 | 1500001 | 2100001 |
| Height | 121 | RAC875_c6922_291 | Q5 | chr4D | 26.97 | 599.51 | 601.28 | 600.33 | 593.75 | 600.11 | 649.53 | 641.04 | 580.64 | 0.30 | 6.2 | 0 | 1000001 | 1300001 |
| Height | 121 | Tdurum_contig42083_1539 | Q7 | chr4D | 3.09 | 610.88 | 620.54 | 608.56 | 609 | 594.23 | 629.3 | 621.7 | 627.37 | 0.23 | 4.09 | 0.04 | 100001 | 200001 |
| Height | 126 | RAC875_c6922_291 | Q5 | chr4D | 26.97 | 635.91 | 639.62 | 634.65 | 629.29 | 636.49 | 688.47 | 678.17 | 617 | 0.34 | 7.59 | 0 | 1000001 | 2100001 |
| Height | 136 | RAC875_c1673_193 | Q4 | chr4D | 32.24 | 665.19 | 672.13 | 664.86 | 668.97 | 670.64 | 748.67 | 752.33 | 655.72 | 0.32 | 6.84 | 0 | 1000001 | 2200001 |
| Height | 148 | RAC875_rep_c105718_585 | Q6 | chr4D | 40.11 | 690.27 | 741 | 689.67 | 695.06 | 699.69 | 826.91 | 798.72 | 687.68 | 0.41 | 10.12 | 0 | 1000001 | 2800001 |
| Height | 158 | RAC875_c1673_193 | Q6 | chr4D | 32.24 | 709.59 | 718.92 | 705.97 | 713.13 | 703.46 | 837.5 | 820.89 | 691.51 | 0.42 | 10.47 | 0 | 1000001 | 2800001 |
| Height | 166 | RAC875_c1673_193 | Q4 | chr4D | 32.24 | 706.59 | 716.82 | 715.03 | 709.11 | 708.93 | 855.32 | 839.75 | 695.3 | 0.40 | 9.62 | 0 | 1000001 | 2500001 |
| Height | 170 | RAC875_c1673_193 | Q4 | chr4D | 32.24 | 711.2 | 723.01 | 711.97 | 709.62 | 708.92 | 860.57 | 835.8 | 693.25 | 0.40 | 9.75 | 0 | 1000001 | 2500001 |
| Height | 180 | RAC875_c1673_193 | Q4 | chr4D | 32.24 | 705.56 | 713.01 | 710.01 | 708.75 | 700.14 | 856.26 | 831.98 | 691.63 | 0.40 | 9.77 | 0 | 1000001 | 2500001 |
| Height | 189 | RAC875_c1673_193 | Q4 | chr4D | 32.24 | 703.12 | 712.39 | 697.06 | 704.36 | 697.64 | 850 | 831.53 | 681.1 | 0.41 | 10.02 | 0 | 1000001 | 2400001 |
| Height | 97 | BS00011360_51 | Q1 | chr5A | 229.67 | 290.19 | 287.85 | 302.31 | 289.38 | 299.26 | 296.85 | 299.37 | 374.83 | 0.31 | 6.16 | 0 | 62700001 | 78500001 |
| TYArea | 166 | Kukri_c27309_590 | Q1 | chr2D | 55.4 | 20203.98 | 18583.62 | 20025.34 | 20084.7 | 18496.39 | 18941.17 | 13170.77 | 19521.4 | 0.25 | 4.2 | 0.03 | 13800001 | 13900001 |
| TYArea | 180 | RAC875_c1673_193 | Q2 | chr4D | 32.24 | 27708.2 | 27568.07 | 27379.38 | 27410.43 | 26809.1 | 38035.26 | 38044.2 | 25882.88 | 0.26 | 4.9 | 0.01 | 1300001 | 2100001 |
| TYArea | 189 | RAC875_c1673_193 | Q2 | chr4D | 32.24 | 36642.01 | 36791.6 | 36739.89 | 37302.61 | 35809.98 | 52920.44 | 51199.04 | 35243 | 0.33 | 7.04 | 0 | 1100001 | 2100001 |
| WA | 158 | GENE_0137_147 | Q1 | chr2D | 53.36 | 242.79 | 233.5 | 237.44 | 241.51 | 240.05 | 244.43 | 203.84 | 241.79 | 0.25 | 4.19 | 0.02 | 12500001 | 13700001 |
| At | BS00087197_51 | chr7B | 253.51 | 3.82 | 3.6 | 3.58 | 4.05 | 3.59 | 2.78 | 3.05 | 3.82 | 0.25 | 4.25 | 0.05 | 74600001 | 74700001 | ||
| B | RAC875_rep_c105718_585 | chr4D | 40.11 | 11.29 | 11.3 | 11.3 | 11.31 | 11.2 | 11.63 | 11.48 | 11.31 | 0.31 | 6.58 | 0 | 1100001 | 2200001 | ||
| Bh | RAC875_c1673_193 | chr4D | 32.24 | 6.53 | 6.54 | 6.52 | 6.55 | 6.54 | 6.75 | 6.68 | 6.52 | 0.38 | 9.09 | 0 | 1100001 | 2500001 |
cM is the marker position. h2 is heritability. logP is –log10 at the QTL peak; chr is the chromosome. P-value is the genome wise P-value for the QTL based on permutations. Alchemy, Brompton, Claire, Hereward, Rialto, Robigus, Soissons and Xi-19 indicate the estimated founder QTL effects as produced by HAPPY. Last two columns show 90% confidence interval (CI) for the QTL based on permutations. These values are island intervals, they are the segments exceeding the genome-wide significance level.