Table 3.
Common quantitative trait nucleotides (QTNs) of root and shoot traits identified using different multi-locus genome-wide association studies (GWAS) methods.
| S. No | QTN | Trait | Marker | Allele | CHR | Physical Position (bp) | LOD Score | R2 (%) | Method |
|---|---|---|---|---|---|---|---|---|---|
| 1 | Q.TRS-2AS | TRS | AX-94952472 | G/C | 2AS | 8181794 | 3.29–3.75 | 9.77–17.72 | 1,5 |
| 2 | Q.TRS-4AL | TRS | AX-95105488 | A/C | 4AL | 631903354 | 3.38–5.01 | 8.82–10.85 | 2,4 |
| 3 | Q.TRS-7BS | TRS | AX-95119337 | G/A | 7BS | 138882791 | 6.81–10.73 | 17.10–22.22 | 2,4 |
| 4 | Q.FOLRN-7AS | FOLRN | AX-95249973 | G/A | 7AS | 54997993 | 3.10–4.92 | 5.22–6.83 | 1,2 |
| 5 | Q.FOLRN-7BS | FOLRN | AX-95123855 | T/C | 7BS | 99635031 | 3.59–4.41 | 6.12–8.62 | 4,5 |
| 6 | Q.SOLRN-1AL | SOLRN | AX-95102105 | A/G | 1AL | 474573230 | 3.24–4.58 | 1.68–3.65 | 1,2,4 |
| 7 | Q.SOLRN-1BL | SOLRN | AX-95077960 | G/A | 1BL | 572301473 | 3.55–8.97 | 2–4.15 | 1,2,4,5 |
| 8 | Q.SOLRN-1DS | SOLRN | AX-94448890 | T/C | 1DS | 10741698 | 4.44–6.92 | 2.47–4.12 | 1,2,4,5 |
| 9 | Q.SOLRN-3BL | SOLRN | AX-94516395 | C/T | 3BL | 738699225 | 4.34–5.58 | 2.61–3.99 | 1,2,4 |
| 10 | Q.SOLRN-3BL | SOLRN | AX-95150666 | G/C | 3BL | 664019441 | 10.31–14.84 | 27.09–38.60 | 1,2,4,5 |
| 11 | Q.SOLRN-3DL | SOLRN | AX-94450588 | A/G | 3DL | 367309893 | 8.17–10.84 | 21.14–26.16 | 4,5 |
| 12 | Q.SOLRN-6AL | SOLRN | AX-95244609 | T/C | 6AL | 599035159 | 4.61–6.78 | 1.88–3.29 | 1,2,4,5 |
| 13 | Q.SOLRN-7BL | SOLRN | AX-94564853 | A/G | 7BL | 673962683 | 4.30–5.98 | 9.92–18.50 | 1,2,4 |
| 14 | Q.SOLRN-7BS | SOLRN | AX-95123855 | T/C | 7BS | 99635031 | 4.49–4.69 | 1.60–2.17 | 4,5 |
| 15 | Q.LRS-2DS | LRS | AX-94471646 | A/G | 2DS | 13929712 | 3.31–7.30 | 1–2.40 | 2,4 |
| 16 | Q.LRS-3AS | LRS | AX-94961347 | C/T | 3AS | 184635201 | 7.15–15.48 | 7.47–12.41 | 1,4,5 |
| 17 | Q.LRS-3BL | LRS | AX-94480990 | G/T | 3BL | 417261367 | 6.63–15.77 | 1–6.15 | 2,4 |
| 18 | Q.LRD-5BS | LRS | AX-94706358 | A/C | 5BS | 69134215 | 3.41–13.25 | 3.47–8.20 | 1,4,5 |
| 19 | Q.LRS-6AL | LRS | AX-95244609 | T/C | 6AL | 599035159 | 3.27–4.21 | 0.12–0.2 | 4,5 |
| 20 | Q.LRD-7BL | LRS | AX-94528392 | G/A | 7BL | 675314495 | 4.92–9.18 | 16.43–30.67 | 1,4,5 |
| 21 | Q.LRD-7BS | LRS | AX-95123855 | T/C | 7BS | 99635031 | 3.35–17.24 | 4.17–8.35 | 1,2,4,5 |
| 22 | Q.LRD-4AL | LRD | AX-94841365 | G/A | 4AL | 725751499 | 4.90–5.56 | 12.04–13.40 | 4,5 |
| 23 | Q.LRD-5DL | LRD | AX-94571501 | T/C | 5DL | 472635782 | 3.46–5.69 | 5.74–11.60 | 3,4,5 |
| 24 | Q.LRD-7BL | LRD | AX-94763902 | T/C | 7BL | 552120841 | 3.58–6.43 | 6.83–10.02 | 2,4,5 |
| 25 | Q.RLD-1BL | RLD | AX-94728516 | T/C | 1BL | 491241476 | 6.01–28.19 | 0.45–4.15 | 4,5 |
| 26 | Q.RLD-2AS | RLD | AX-94952472 | G/C | 2AS | 8181794 | 3.67–9.52 | 0.98–4.23 | 4,5 |
| 27 | Q.RLD-3BS | RLD | AX-94516395 | C/T | 3BL | 738699225 | 3.36–3.46 | 1.66–1.93 | 4,5 |
| 28 | Q.RLD-3DL | RLD | AX-94544285 | C/G | 3DL | 594478810 | 5.88–21.54 | 3.94–6.33 | 2,4 |
| 29 | Q.RLD-4AL | RLD | AX-95105488 | A/C | 4AL | 631903354 | 3.26–8.06 | 5.97–15.44 | 1,4 |
| 30 | Q.RLD-5AL | RLD | AX-95659861 | G/A | 5AL | 565754230 | 3.49–6.68 | 1.89–2.57 | 2,5 |
| 31 | Q.RLD-5DS | RLD | AX-95160709 | G/T | 5DS | 10471964 | 3.49–13.73 | 0.16–4.38 | 4,5 |
| 32 | Q.RLD-6BL | RLD | AX-94502864 | G/A | 6BL | 710324542 | 9.73–14.54 | 1.14–8.22 | 4,5 |
| 33 | Q.RLD-7BS | RLD | AX-95119337 | G/A | 7BS | 138882791 | 6.71–11.23 | 12.20–17.08 | 1,4,5 |
| 34 | Q.AD-1AL | AD | AX-94932678 | A/G | 1AL | 557954056 | 3.67–6.82 | 2.42–5.92 | 4,5 |
| 35 | Q.AD-1BL | AD | AX-94620468 | A/G | 1BL | 586302698 | 5.16–8.86 | 3.31–7.79 | 2,4,5 |
| 36 | Q.AD-1BS | AD | AX-94668789 | G/A | 1BS | 96515530 | 3.67–5.97 | 0.17–1.53 | 2,5 |
| 37 | Q.AD-2DL | AD | AX-94647816 | A/C | 2DL | 641980126 | 4.58–22.75 | 3.53–7.08 | 2,4 |
| 38 | Q.AD-3AS | AD | AX-94996868 | C/T | 3AS | 1030506 | 6.25–16.45 | 1.67–8.54 | 2,4 |
| 39 | Q.AD-3BS | AD | AX-94886515 | T/C | 3BS | 129437930 | 3.90–9.27 | 1.55–2.72 | 2,5 |
| 40 | Q.AD-3DS | AD | AX-94726849 | C/T | 3DS | 81391081 | 6.70–7.87 | 0.21–2.18 | 2,4 |
| 41 | Q.AD-4AL | AD | AX-94740863 | T/C | 4AL | 725802675 | 3.10–5.14 | 0.12–3.54 | 4,5 |
| 42 | Q.AD-6AL | AD | AX-95244609 | T/C | 6AL | 599035159 | 3.38–10.62 | 3.03–5.88 | 2,3,4,5 |
| 43 | Q.AD-6BS | AD | AX-94691127 | G/A | 6BS | 288419550 | 4.97–5.80 | 0.18–1.28 | 4,5 |
| 44 | Q.AD-6DL | AD | AX-94853162 | G/A | 6DL | 470294593 | 3.70–4.51 | 0.39–1.65 | 4,5 |
| 45 | Q.RV-2BS | RV | AX-95227366 | G | 2BS | 46089220 | 3.25–1152.63 | 11.40–13.56 | 1,2,4 |
| 46 | Q.RV-4AL | RV | AX-95105488 | A/C | 4AL | 631903354 | 3.97–1166.09 | 2.06–8.08 | 1,2,3 |
| 47 | Q.RV-4BS | RV | AX-94648074 | C/T | 4BS | 140929724 | 3.45–1122.58 | 2.72–4.81 | 1,2,4 |
| 48 | Q.RV-5BL | RV | AX-94439232 | C/A | 5BL | 287624152 | 3.80–1152.24 | 1.47–5.31 | 1,2,4,5 |
| 49 | Q.RV-6AL | RV | AX-95162623 | C/T | 6AL | 611851405 | 3.76–7.56 | 0.18–2.61 | 4,5 |
| 50 | Q.RV-6AS | RV | AX-94687596 | A/G | 6AS | 959041 | 5.10–7.87 | 0.97–2.20 | 4,5 |
| 51 | Q.RV-6AS | RV | AX-94893701 | A/G | 6AS | 24857477 | 5.21–9.45 | 0.70–1.23 | 4,5 |
| 52 | Q.RV-6BL | RV | AX-94502864 | G/A | 6BL | 710324542 | 4.54–1136.81 | 0.52–5.93 | 2,4,5 |
| 53 | Q.RV-7AL | RV | AX-94664277 | C/T | 7AL | 689920746 | 4.61–1155.16 | 5.53–11.20 | 1,2,4,5 |
| 54 | Q.SRN-2DL | SRN | AX-94551988 | A/G | 2DL | 579965138 | 4.27–7.94 | 6.83–17.74 | 1,3,4,5 |
| 55 | Q.SRN-3BS | SRN | AX-94486290 | T/C | 3BL | 477885835 | 5.68–6.68 | 5.82–6.51 | 1,2 |
| 56 | Q.SRN-3DL | SRN | AX-94382595 | C/T | 3DL | 392956661 | 3.19–4.40 | 0.31–8.32 | 2,4 |
| 57 | Q.SRN-4DL | SRN | AX-95157799 | A/G | 4DL | 461218017 | 5.66–7.19 | 17.38–20.91 | 1,2 |
| 58 | Q.SRN-6AL | SRN | AX-94637211 | A/G | 6AL | 611576606 | 3.08–4.87 | 11.77–14.95 | 1,2 |
| 59 | Q.SRN-6AL | SRN | AX-94790960 | C/A | 6AL | 600131055 | 6.19–9.13 | 23.20–28.08 | 1,2 |
| 60 | Q.SDW-3DS | SDW | AX-94439998 | T/C | 3DS | 85060915 | 4.29–4.29 | 8.15–9.74 | 1,2 |
| 61 | Q.SDW-4AL | SDW | AX-94470023 | T/C | 4AL | 581216490 | 4.49–6.61 | 8.09–19.05 | 1,2,3,4,5 |
| 62 | Q.SDW-4BS | SDW | AX-95630040 | A/G | 4BS | 12893614 | 3.25–8.40 | 5.43–11.57 | 3,4,5 |
| 63 | Q.SDW-5BL | SDW | AX-94484139 | T/C | 5BL | 289567014 | 4.72–4.87 | 5.64–5.92 | 4,5 |
| 64 | Q.SDW-7AL | SDW | AX-94664277 | C/T | 7AL | 689920746 | 3.36–4.03 | 4.39–5.30 | 4,5 |
| 65 | Q.SDW-7BL | SDW | AX-95165787 | C/A | 7BL | 591053449 | 3.11–3.13 | 6.54–7.06 | 4,5 |
| 66 | Q.RDW-1BL | RDW | AX-94925225 | T/C | 1BL | 372996241 | 4.49–4.97 | 4.87–7.59 | 4,5 |
| 67 | Q.RDW-5AL | RDW | AX-94501549 | C/T | 5AL | 672339596 | 4.29–4.91 | 4.71–7.45 | 2,3,4 |
| 68 | Q.RDW-6AS | RDW | AX-94809955 | C/T | 6AS | 631698 | 4.67–5.39 | 4.37–5.67 | 2,4 |
| 69 | Q.RDW-7AS | RDW | AX-94386260 | G/A | 7AS | 269093921 | 3.65–4.35 | 18.35–18.60 | 1,2 |
| 70 | Q.SL-1AL | SL | AX-94929421 | T/C | 1AL | 550331092 | 5.63–5.66 | 5.16–5.39 | 1,2 |
| 71 | Q.SL-2AL | SL | AX-95076063 | T/C | 2AL | 555820355 | 3.52–4.91 | 3.68–8.24 | 1,3,5 |
| 72 | Q.SL-4BS | SL | AX-95012217 | C/T | 4BS | 97922535 | 4.71–6.36 | 5.06–5.74 | 1,5 |
| 73 | Q.SL-5BL | SL | AX-95092434 | C/G | 5BL | 579153579 | 4.16–5.20 | 5.57–8.61 | 1,2 |
| 74 | Q.SL-7BS | SL | AX-94876335 | G/A | 7BS | 144484919 | 4.04–5.48 | 7.23–8.27 | 1,2 |
| 75 | Q.RL-1DS | RL | AX-94448890 | T/C | 1DS | 10741698 | 4.02–5.52 | 3.67–7.89 | 1,2,5 |
| 76 | Q.RL-2BS | RL | AX-95227366 | G | 2BS | 46089220 | 3.68–5.77 | 8.59–15.76 | 1,4 |
| 77 | Q.RL-6BL | RL | AX-94502864 | G/A | 6BL | 710324542 | 4.63–6.06 | 4.68–9.41 | 1,2,3,4,5 |
| 78 | Q.RL-6BS | RL | AX-94539094 | A/C | 6BS | 8387528 | 3.52–6.77 | 2.83–17.15 | 1,2,5 |
| 79 | Q.RL-6BS | RL | AX-94900754 | A/G | 6BS | 157792843 | 3.27–5.44 | 5.26–9.16 | 1,3 |
| 80 | Q.RL-7AL | RL | AX-95241843 | G/T | 7AL | 610498024 | 6.31–6.50 | 5.55–5.97 | 1,2 |
| 81 | Q.RL-7BL | RL | AX-94528392 | G/A | 7BL | 675314495 | 3.21–8.52 | 15.42–30.83 | 1,5 |
| 82 | Q.RL-7DL | RL | AX-94861078 | A/G | 7DL | 614276051 | 3.36–5.01 | 3.12–4.24 | 3,4 |
| 83 | Q.RSDWR-2AL | RSDWR | AX-94430108 | C/T | 2AL | 509357786 | 5.19–14.68 | 0.55–1.38 | 2,4 |
| 84 | Q.RSDWR-2BL | RSDWR | AX-94856412 | C/T | 2BL | 754864363 | 4.85–103.96 | 0.58–1.95 | 4,5 |
| 85 | Q.RSDWR-3BS | RSDWR | AX-94691217 | A/G | 3BS | 8029967 | 8.14–83.91 | 0.02–3.22 | 2,4 |
| 86 | Q.SRL-5AL | SRL | AX-94748697 | A/G | 5AL | 406534846 | 3.37–6.01 | 4.81–8.10 | 2,4,5 |
| 87 | Q.SRL-2BL | SRL | AX-94457792 | T/C | 2BL | 576083471 | 8.12–19.40 | 64.33–31.92 | 1,2,4,5 |
TRS, total root size (cm); FOLRN, first order lateral root number; SOLRN, second order lateral root number; LRS, lateral root size; LRD, lateral root density (cm−1); RLD, root length density cm−2; AD, average diameter (mm); RV, root volume (cm3); SRN, seminal root number; SDW, shoot dry weight (mg); RDW, root dry weight (mg); SL, shoot length (cm); RL, root length (cm); RSDWR, root shoot dry weight ratio; SRL, specific root length (cm mg−1). ML-GWAS methods (MrMLM-1, FASTMrMLM-2, FASTMrEMMA-3, pLARmEB-4, ISIS EM-BLASSO-5).