Table 1 Sixty-one QTNs identified using two or more than two multi-locus GWAS models. logarithm of the odds (LOD) and phenotypic variance explained (R2%) for each QTN are also reported. Trait acronym are reported in Supplementary Table 3
S. No | QTN | Trait | Marker | Allele | Physical position (bp) | LOD | R2 (%) | Method |
|---|---|---|---|---|---|---|---|---|
1 | Q.Adf-1B | ADF | GENE-0173_168 | A/G | 1B: 293,176,664 | 3.62–3.62 | 3.57–3.57 | 1,5 |
2 | Q.Adf-3B | ADF | Kukri_c22235_1547 | G/T | 3B: 786,404,075 | 3.52–6.85 | 3.72–8.77 | 2,3,5,6 |
3 | Q.Adf-5A | ADF | Kukri_rep_c101981_260 | G/T | 5A: 319,304,864 | 3.19–4.27 | 1.47–10.05 | 2,4,6 |
4 | Q.Adl-2B.1 | ADL | BobWhite_c30140_119 | A/G | 2B: 745,946,175 | 4.10–5.35 | 2.77–8.48 | 1,2 |
5 | Q.Adl-2B.2 | ADL | wsnp_Ex_c24135_33382521 | A/G | 2B: 702,731,805 | 3.04–10.79 | 3.90–17.42 | 1,2,3,4,5 |
6 | Q.Cel-2A | CEL | Ku_c8927_2075 | C/T | 2A: 685,865,037 | 8.87–5.51 | 6.71–14.74 | 1,5 |
7 | Q.Cel-3A.1 | CEL | BobWhite_c38444_238 | G/T | 3A: 676,958,917 | 3.06–3.16 | 0.56–1.70 | 5,6 |
8 | Q.Cel-3A.2 | CEL | BS00048633_51 | A/G | 3A: 722,371,044 | 3.04–4.76 | 3.32–6.65 | 1,2,3 |
9 | Q.Cel-4A | CEL | Excalibur_c24511_1196 | A/G | 4A: 607,877,731 | 3.30–8.16 | 2.90–7.73 | 1,4,6,5 |
10 | Q.Ttn-2A | TTN | BS00068050_51 | C/T | 2A: 7,171,528 | 3.04–4.36 | 0.29–4.81 | 1,2,4 |
11 | Q.Ttn-2B | TTN | Tdurum_contig74936_456 | A/G | 2B: 79,054,183 | 3.29–6.82 | 0.00–7.87 | 4,6 |
12 | Q.Ttn-7A | TTN | Kukri_c18148_913 | C/T | 7A: 715,952,715 | 3.30–4-84 | 2.32–8.80 | 1,3 |
13 | Q.Hi-4A | HI | Tdurum_contig42638_383 | A/C | 4A: 727,573,605 | 3.18–9.11 | 1.22–20.94 | 1,2,6 |
14 | Q.Hi-7A.1 | HI | BS00044593_51 | A/G | 7A: 123,464,462 | 5.41–7.82 | 0.12–6.04 | 5,6 |
15 | Q.Hi-7A.2 | HI | RFL_Contig2834_890 | C/T | 7A: 714,390,256 | 3.33–5.73 | 1.60–5.05 | 2,5,6 |
16 | Q.HI-7B | HI | RAC875_c48671_172 | A/G | 7B: 719,682,848 | 3.17–3.87 | 1.10–1.59 | 5,6 |
17 | Q.Biomass-2B.1 | BIOMASS | Excalibur_c34937_710 | G/T | 2B: 6,711,112 | 3.42–6.85 | 8.49–14.79 | 1,5,6 |
18 | Q.Biomass-2B.2 | BIOMASS | RAC875_c31214_58 | C/T | 2B: 770,956,440 | 4.30–5.48 | 5.99–7.77 | 1,5,6 |
19 | Q.Biomass-4B | BIOMASS | RAC875_c25045_637 | C/T | 4B: 548,976,483 | 3.21–3.98 | 6.32–10.91 | 1,2,5,6 |
20 | Q.Biomass-5A | BIOMASS | wsnp_Ex_c1138_2185522 | A/G | 5A: 533,045,040 | 3.13–5.67 | 0.00–8.00 | 1,6 |
21 | Q.Gw-4A | GW | Ra_c1897_2401 | C/T | 4A: 702,329,094 | 3.73–6.89 | 4.82–11.00 | 1,2,3,6 |
22 | Q.Gw-7B | GW | BS00068071_51 | A/G | 7B: 173,518,366 | 3.28–3.56 | 0.00–8.47 | 2,6 |
23 | Q.Ndf-2A | NDF | Tdurum_contig31185_456 | C/T | 2A: 741,540,226 | 3.78–4.30 | 3.81–5.58 | 2,3,6 |
24 | Q.Ndf-4B.1 | NDF | BS00024110_51 | G/T | 4B: 89,594,936 | 3.34–4.15 | 0.00–10.34 | 2,5,6 |
25 | Q.Ndf-4B.2 | NDF | BS00030571_51 | A/G | 4B: 606,290,375 | 3.69–7.23 | 3.67–8.11 | 2,5,6 |
26 | Q.Ndf-7A | NDF | BobWhite_c25527_980 | C/T | 7A: 709,196,631 | 3.38–4.46 | 0.00–1.01 | 2,5 |
27 | Q.Scsa-1A.1 | SCSa | BS00110627_51 | G/T | 1A: 527,767,957 | 4.09–6.14 | 6.51–7.76 | 3,5 |
28 | Q.Scsa-1A.2 | SCSa | Tdurum_contig51833_439 | A/G | 1A: 537,137,625 | 3.62–7.12 | 10.68–13.16 | 1,4,6 |
29 | Q.Scsa-2A | SCSa | GENE-1381_110 | G/T | 2A: 685,560,391 | 3.25–4.02 | 1.52–4.81 | 1,4,6 |
30 | Q.Scsa-3A | SCSa | RAC875_c3084_415 | C/T | 3A: 728,749,058 | 4.53–6.16 | 12.00–15.55 | 1,6 |
31 | Q.Scsa-3B | SCSa | BS00059887_51 | A/G | 3B: 748,418,401 | 3.24–5.67 | 0.00–9.96 | 1,2 |
32 | Q.Scsa-6A | SCSa | BS00068218_51 | C/T | 6A: 599,877,040 | 3.58–5.09 | 2.31–6.24 | 1,2,4 |
33 | Q.Scsm-1A | SCSm | wsnp_Ex_c4186_7560575 | C/T | 1A: 584,664,979 | 3.48–3.96 | 2.70–3.54 | 2,5 |
34 | Q.Scsm-2B | SCSm | BS00025649_51 | A/C | 2B: 704,739,952 | 3.33–4.84 | 5.58–6.59 | 1,2 |
35 | Q.Scsm-3B | SCSm | RAC875_c63132_298 | C/T | 3B: 6,886,640 | 4.11–4.51 | 7.62–11.95 | 4,6 |
36 | Q.Scsm-4A | SCSm | RAC875_c18732_193 | G/T | 4A: 380,699,504 | 4.11–9.09 | 5.74–12.14 | 1,2,5,6 |
37 | Q.Scsm-6B.1 | SCSm | BS00011192_51 | A/G | 6B: 681,643,033 | 3.34–3.64 | 5.12–7.39 | 1,6 |
38 | Q.Scsm-6B.2 | SCSm | RAC875_c49329_81 | C/T | 6B: 684,859,721 | 3.36–4.67 | 5.48–7.75 | 4,5 |
39 | Q.Scsm-6B.3 | SCSm | wsnp_BF293311B_Ta_2_3 | A/C | 6B: 439,365,045 | 4.43–4.73 | 7.23–10.44 | 1,2 |
40 | Q.Scsm-6B.4 | SCSm | Excalibur_c64119_578 | C/T | 6B: 12,368,785 | 5.22–5.83 | 7.97–10.88 | 1,2,4,5 |
41 | Q.Scsb-2B | SCSb | Excalibur_c10068_1276 | A/G | 2B: 743,736,881 | 4.92–9-32 | 8.55–19.14 | 1,2,3 |
42 | Q.Scsb-3B | SCSb | RFL_Contig3228_2154 | C/T | 3B: 21,113,077 | 3.81–8.78 | 8.96–13.11 | 1,2,3,4,6 |
43 | Q.Scsb-4A | SCSb | Tdurum_contig15260_650 | A/G | 4A: 721,237,375 | 3.05–3.11 | 5.21–6.06 | 1,2 |
44 | Q.Scsb-6A.1 | SCSb | wsnp_Ku_c26784_36748247 | C/T | 6A: 50,651,609 | 3.07–4,07 | 1.90–2.20 | 4,6 |
45 | Q.Scsb-6A.2 | SCSb | BS00036878_51 | A/G | 6A: 452,642,718 | 3.43–4.95 | 0.00–1.65 | 2,4,6 |
46 | Q.Hem-4B | HEM | BS00003765_51 | C/T | 4B: 601,823,368 | 3.78–5.03 | 2.13–4.76 | 3,5 |
47 | Q.Hem-5A | HEM | Ra_c19494_275 | C/T | 5A: 625,718,974 | 4.38–7.19 | 4.53–3.34 | 5,6 |
48 | Q.Hem-6B | HEM | RAC875_c47035_70 | A/G | 6B: 442,960,966 | 3.14–5.69 | 0.00–7.19 | 4,5,6 |
49 | Q.Spl-1A.1 | SPL | D_GBUVHFX01API9H_416 | A/G | 1A: 560,604,148 | 7.13–12.54 | 5.72–11.96 | 1,2 |
50 | Q.Spl-1A.2 | SPL | BobWhite_c44947_277 | C/T | 1A: 580,573,915 | 3.08–7.44 | 2.43–6.39 | 1,2,3,4,5,6 |
51 | Q.Spl-3B | SPL | Tdurum_contig12087_190 | A/C | 3B: 736,504,198 | 5.85–7.87 | 10.33–12.68 | 1,3 |
52 | Q.Spl-4A.1 | SPL | RAC875_c34515_343 | A/G | 4A: 617,606,418 | 3.84–5.41 | 1.87–4.76 | 1,4 |
53 | Q.Spl-4A.2 | SPL | Tdurum_contig47858_908 | A/G | 4A: 618,975,358 | 5.04–8.08 | 2.36–3.60 | 4,6,5 |
54 | Q.Spl-4B.1 | SPL | Ex_c14614_433 | A/G | 4B: 114,625,178 | 4.51–8.48 | 4.86–7.91 | 3,6 |
55 | Q.Spl-4B.2 | SPL | Excalibur_c12937_544 | A/G | 4B: 654,334,669 | 4.97–9.87 | 4.73–9.25 | 1,6 |
56 | Q.Spl-4B.3 | SPL | Excalibur_rep_c70127_360 | A/G | 4B: 560,440,302 | 3.22–11.65 | 0.00–9.03 | 1,2,4 |
57 | Q.Spl-6A | SPL | GENE-3665_61 | A/G | 6A: 36,191,483 | 3.41–4.04 | 1.86–1.86 | 2,6 |
58 | Q.Spl-7A | SPL | wsnp_Ku_c792_1635653 | C/T | 7A: 9,266,099 | 4.54–4.73 | 3.04–3.55 | 5,6 |
59 | Q.Ftn-2B | FTN | Excalibur_c27769_1089 | C/T | 2B: 135,830,179 | 3.04–5.82 | 0.37–1.11 | 2,6 |
60 | Q.Ftn-5A | FTN | BS00000365_51 | A/G | 5A: 501,011,928 | 5.72–11.41 | 3,12–5.10 | 2,6 |
61 | Q.Ftn-6A | FTN | Kukri_c45702_439 | A/G | 6A: 602,501,261 | 4.37–6.03 | 0.96–2.12 | 2,6 |
62 | Q.Ph-1A | PH | Excalibur_c6255_1119 | T/C | 1A: 152,822,081 | 12.02–16.10 | 12.45–19.78 | 1,5 |
63 | Q.Ph-2A.1 | PH | BS00089497_51 | G/A | 2A: 688,361,342 | 5.30–6.54 | 2.09–2.55 | 1,2,3,4 |
64 | Q.Ph-2A.2 | PH | CAP12_rep_c6956_169 | T/C | 2A: 691,749,827 | 4.32–7.61 | 1.20–2.04 | 2,3 |
65 | Q.Ph-2A.3 | PH | BS00107804_51 | C/T | 2A: 701,377,125 | 4.48–5.36 | 1.69–2.89 | 4,6 |
66 | Q.Ph-3A | PH | wsnp_Ex_c20250_29303152 | G/T | 3A: 687,446,416 | 3.95–14.09 | 2.30.7.37 | 3,6 |
67 | Q.Ph-4B.1 | PH | BS00023766_51 | T/C | 4B: 30,278,520 | 4.26–7.99 | 2.10–4.18 | 3,6 |
68 | Q.Ph-4B.2 | PH | Tdurum_contig63670_287 | G/A | 4B: 35,030,729 | 4.29–17.11 | 3.79–9.61 | 1,2,4,5 |
69 | Q.Ph-5B.1 | PH | RAC875_c39204_91 | C/T | 5B: 23,191,553 | 5.17–12.82 | 2.76–6.47 | 1,4,5 |
70 | Q.Ph-5B.2 | PH | BS00068200_51 | T/C | 5B: 510,428,487 | 3.89–6.75 | 1.67–2.84 | 2,3 |
71 | Q.Ph-7A | PH | RAC875_c28585_156 | C/T | 7A: 16,934,067 | 4.21–4.72 | 1.51–1.87 | 2,3 |
72 | Q.Ph-7B | PH | BobWhite_rep_c49050_1890 | A/G | 7B: 622,291,386 | 3.99–9.81 | 0.93–2.73 | 2,4,6 |