Table 3.
Details of loci associated with photosynthesis-related traits via multi-locus GWAS in soybean.
| Region associateda | Chr.b | SNP associatedc | Pos. (bp)d | No.e | LOD | r2 (%)f | Position intervals (bp) | Methodg | Trait-year-treatmenth |
|---|---|---|---|---|---|---|---|---|---|
| q1-1 | 1 | AX-93961332 | 951461 | 5 | 6.32 | 3.35 | 951461–1344144 | 1, 3, 5 | TrLP_E1, CoLP_E1, TrL/NP_E2, CoL/NP_E1 |
| q1-2 | 1 | AX-93675249 | 50496989 | 1 | 11.37 | 8.83 | 50496989 | 1, 2, 3 | PnLP_E2, PnNP_E2 |
| q6 | 6 | AX-93728015 | 12548698 | 7 | 9.18 | 11.51 | 12516126–12966564 | 1, 2, 3, 4, 5 | TrLP_E1, CoLP_E2, TrNP_E2, CoNP_E2, TrL/NP_E2, CoL/NP_E2 |
| q7-1 | 7 | AX-93926489 | 3402895 | 4 | 7.68 | 11.06 | 1787229– 3402895 | 1, 3, 5 | CiLP_E2, CoL/NP_E1, CiL/NP_E1 |
| q7-2 | 7 | AX-93741303 | 9520676 | 7 | 6.55 | 4.46 | 6578651– 9520676 | 1, 2, 3, 5 | PnLP_E2, CiLP_E2, TrNP_E2, CoNP_E2, TrL/NP_E1, CoL/NP_E1, CoL/NP_E2 |
| q8-1 | 8 | AX-93753054 | 11620180 | 7 | 7.82 | 6.41 | 6955757–11620180 | 1, 2, 3, 4, 5 | PnLP_E2, TrLP_E1, CoLP_E1, PnNP_E1, CoNP_E1, CoNP_E2, TrL/NP_E1, |
| q8-2 | 8 | AX-93929582 | 27620272 | 1 | 6.54 | 3.19 | 27620272 | 1, 2, 3, 4 | PnLP_E2, PnNP_E2 |
| q8-3 | 8 | AX-93759645 | 43743823 | 6 | 9.87 | 9.64 | 41226360–46081608 | 1, 2, 4, 5, 6 | PnNP_E1, PnNP_E2, TrNP_E2, CoNP_E2, CiNP_E2, TrL/NP_E1, CoL/NP_E1, CiL/NP_E2 |
| q9 | 9 | AX-94066868 | 40240035 | 6 | 12.20 | 13.77 | 40188126–42709534 | 1, 2, 3, 4, 5 | TrLP_E2, CoLP_E2, TrNP_E1, CoNP_E2, CiNP_E1, TrL/NP_E1, TrL/NP_E2, CiNP_E2 |
| q11-1 | 11 | AX-94084631 | 6262749 | 4 | 8.13 | 7.09 | 6262749–9894114 | 2, 4, 5 | PnNP_E1, PnNP_E2, CoL/NP_E2, CiL/NP_E1 |
| q11-2 | 11 | AX-94091690 | 32599188 | 4 | 6.92 | 9.87 | 32540598–34020885 | 2, 3, 4, 5 | TrNP_E1, CoNP_E1, CiNP_E2, CoL/NP_E2, CiL/NP_E2 |
| q12 | 12 | AX-93796430 | 1697221 | 2 | 8.18 | 7.24 | 613090–1697221 | 1, 3, 4, 5 | CiNP_E2, CiL/NP_E2 |
| q13-1 | 13 | AX-94104819 | 18590366 | 4 | 28.95 | 6.31 | 15071765–18590366 | 1, 2, 3, | TrLP_E1, CoLP_E1, CiLP_E1, PnNP_E1, CiNP_E1, CoNP_E1, CoL/NP_E2 |
| q13-2 | 13 | AX-94287210 | 31003637 | 5 | 10.38 | 1.28 | 29481274–31003637 | 1, 3, 4, 5 | PnNP_E2, TrNP_E2, PnL/NP_E1, TrL/NP_E1, CiL/NP_E1, CiL/NP_E2 |
| q14-1 | 14 | AX-93820315 | 1059966 | 5 | 9.24 | 7.03 | 1059966–2165525 | 1, 2, 4, 5, 6 | PnLP_E2, PnNP_E2, TrL/NP_E2, CoL/NP_E2, CiL/NP_E2 |
| q14-2 | 14 | AX-94288085 | 4897088 | 4 | 21.44 | 7.25 | 4897088–7755174 | 1, 3, 4, 5 | CoLP_E2, CiLP_E2, TrNP_E2, CoNP_E2, TrL/NP_E2 |
| q14-3 | 14 | AX-94129538 | 47514182 | 7 | 7.27 | 5.19 | 46008634–47723841 | 2, 3, 4, 5 | PnLP_E1, CoLP_E1, PnL/NP_E1, PnL/NP_E2, TrL/NP_E1, CiL/NP_E2 |
| q15-1 | 15 | AX-94134672 | 12611721 | 3 | 6.26 | 2.32 | 12227172–12611721 | 1, 3, 4 | CoLP_E2, CoNP_E1, CoNP_E2, PnL/NP_E1 |
| q15-2 | 15 | AX-93841986 | 35259050 | 2 | 7.39 | 5.01 | 33719705–35259050 | 1, 2, 4, 5 | PnLP_E2, TrLP_E2, CoLP_E2 |
| q16-1 | 16 | AX-93946322 | 179538 | 5 | 6.73 | 5.10 | 147918–2435036 | 1, 2, 4, 5 | TrNP_E2, CoNP_E1, CoNP_E2, CiNP_E2 |
| q16-2 | 16 | AX-93947209 | 35210924 | 7 | 10.99 | 7.30 | 32784699–37003959 | 1, 2, 4, 5 | TrLP_E1, TrLP_E2, CoLP_E1, CoLP_E2, CoL/NP_E2 |
| q17-1 | 17 | AX-94155900 | 5718961 | 4 | 11.38 | 9.51 | 5718961–5761052 | 2, 3, 5 | CoLP_E2, PnNP_E1, TrNP_E2, CiL/NP_E1 |
| q17-2 | 17 | AX-94159333 | 15188572 | 2 | 7.19 | 8.91 | 15188572–15492731 | 2, 3, 4, 5 | CiLP_E1, CiNP_E1 |
| q17-3 | 17 | AX-93866265 | 37701731 | 5 | 8.32 | 9.24 | 37615577–39224452 | 1, 2, 3, 4 | TrLP_E1, PnNP_E1, TrNP_E2, TrL/NP_E2, CoL/NP_E2 |
| q18-1 | 18 | AX-94166205 | 2982489 | 7 | 15.10 | 12.61 | 674420–3925002 | 2, 3, 4, 5 | PnLP_E1, TrLP_E1, CiLP_E1, CiLP_E2, CiNP_E1, TrL/NP_E2 |
| q18-2 | 18 | AX-93871255 | 9956907 | 6 | 9.86 | 15.88 | 5443584-9956907 | 1, 2, 3, 4, 5 | PnLP_E1, TrLP_E1, TrLP_E2, CoLP_E2, PnNP_E2, CoL/NP_E1 |
| q18-3 | 18 | AX-93883305 | 53037663 | 15 | 13.24 | 10.91 | 50663235- 55727445 | 1, 2, 3, 5, 6 | PnLP_E2, TrLP_E2, CoLP_E1, PnNP_E2, CoNP_E1, CoNP_E2, PnL/NP_E1, TrL/NP_E1, CoL/NP_E1, CiL/NP_E1, CiL/NP_E2 |
| q19 | 19 | AX-93886366 | 2991135 | 4 | 8.17 | 9.02 | 2991135- 3374702 | 1, 4, 5, 6 | TrLP_E1, TrLP_E2, CoLP_E1, CoLP_E2 |
| q20-1 | 20 | AX-94197533 | 1364621 | 6 | 8.20 | 6.22 | 455608-3145850 | 2, 3, 4, 5 | CoLP_E1, PnL/NP_E1, TrL/NP_E1, TrL/NP_E2, CoL/NP_E1, CiL/NP_E2 |
| q20-2 | 20 | AX-93956837 | 35089898 | 10 | 11.48 | 16.82 | 35089898-39987379 | 1, 2, 3, 5, 6 | PnLP_E1, TrLP_E1, CoLP_E1, CiLP_E1, PnNP_E1, CoNP_E1, PnL/NP_E2, TrL/NP_E1, TrL/NP_E2, CoL/NP_E2 |
| q20-3 | 20 | AX-93910666 | 45122261 | 4 | 8.91 | 7.38 | 44049520- 46908248 | 1, 2, 3, 4 | TrNP_E1, CoNP_E1, CiNP_E2, CoL/NP_E2 |
a
QTN named by chromosome.
b
Chromosome.
c
QTNs that were significantly associated with the trait.
d
QTN position (bp) on soybean genome assembly Glycine max Wm82.a1.v1.1 (www.phytozome.net).
e
The number of significant QTNs detected in the region.
f
The proportion of phenotypic variance explained by each QTN.
g
The mrMLM, pKWmEB, pLARmEB, FASTmrMLM, ISIS EM-BLASSO, and FASTmrEMMA were marked from 1 to 6, respectively.
h
The trait-year-treatment combination of QTN, for example, Pn, net photosynthetic rate; Tr, transpiration rate; Ci, intercellular carbon dioxide concentration; and Co, stomatal conductance; followed by the treatments and environments. NP, LP and L/NP denote normal-P, low-P and the ratio of low/normal P condition, respectively. E1 and E2 denote 2015 and 2016, respectively.
The bold values denote major QTL.