TABLE 4.
Significant SNPs associated with root and shoot related traits detected by GWAS.
| Trait | Position | Methoda | Stageb | Chr | P-value | -log10(P) | R2 | Allele | Count | MAF |
| TPB | 4653989 | 1 | 1 | Chr08 | 8.10E-05 | 4.09 | 0.251 | T/C | T:116_C:22 | 0.16 |
| TRL | 4673257 | 4 | 1 | Chr08 | 3.70E-05 | 4.43 | 0.252 | C/G | C:123_G:21 | 0.15 |
| BN | 9585410 | 1 | 3 | Chr18 | 1.22E-05 | 4.92 | 0.301 | G/C | G:110_C:6 | 0.05 |
| BN | 11071047 | 5, 4 | 2 | Chr02 | 6.17E-05 | 4.21 | 0.300 | G/C | G:100_C:18 | 0.15 |
| SA | 12157467 | 4, 5 | 3 | Chr06 | 2.18E-05 | 4.66 | 0.323 | T/C | T:79_C:65 | 0.45 |
| SA | 12684509 | 4, 1, 5 | 2,3 | Chr04 | 9.8E-05 | 4.01 | 0.238 | A/T | A:93_T:45 | 0.33 |
| RDW/SDW | 29621947 | 2, 3, 1 | 1 | Chr16 | 1.08E-08 | 7.97 | 0.721 | C/A | C:113_A:15 | 0.12 |
| SDW | 30444845 | 2,1,4,5 | 2,3 | Chr13 | 7.1E-05 | 4.15 | 0.260 | T/C | T:130_C:8 | 0.06 |
| SDW | 30444857 | 2,1,4,5 | 2,3 | Chr13 | 7.1E-05 | 4.15 | 0.260 | G/A | G:130_A:8 | 0.06 |
| SDW | 30444862 | 5,1,2,4 | 2,3 | Chr13 | 1.2E-05 | 4.92 | 0.240 | A/G | A:130_G:8 | 0.06 |
| SDW | 30444865 | 4,1,2,5 | 2,3 | Chr13 | 7.4E-06 | 5.13 | 0.354 | C/T | C:130_T:8 | 0.06 |
| SDW | 30444924 | 1,2,4,5 | 2,3 | Chr13 | 9.6E-05 | 4.02 | 0.207 | C/T | C:130_T:8 | 0.06 |
| RV, SDW, TPB | 30887365 | 4, 5 | 2,3 | Chr13 | 2.3E-05 | 4.64 | 0.234 | A/T | A:123_T:11 | 0.08 |
| RV | 30910036 | 1 | 2,3 | Chr13 | 6.1E-05 | 4.22 | 0.210 | C/T | C:114_T:18 | 0.14 |
| SA | 30910036 | 5, 4 | 2,3 | Chr13 | 5.2E-05 | 4.29 | 0.212 | C/T | C:114_T:18 | 0.14 |
| RV | 30910036 | 4, 1, 5 | 2,3 | Chr13 | 6.1E-05 | 4.07 | 0.253 | C/T | C:114_T:18 | 0.14 |
| SL | 31398594 | 1, 4 | 2,3 | Chr09 | 7.8E-05 | 4.11 | 0.228 | T/C | T:118_C:8 | 0.06 |
| TRL | 33383414 | 4 | 2 | Chr16 | 2.08E-05 | 4.68 | 0.213 | G/T | G:76_T:68 | 0.47 |
| RDW/SDW | 36801463 | 5, 4 | 1 | Chr16 | 1.26E-05 | 4.90 | 0.253 | T/A | T:133_A:9 | 0.06 |
| SDW | 37605828 | 4 | 2 | Chr09 | 9.04E-05 | 4.04 | 0.250 | C/T | C:76_T:64 | 0.46 |
| SDW | 40092616 | 1, 2 | 3 | Chr13 | 1.30E-06 | 5.89 | 0.345 | C/G | C:105_G:31 | 0.23 |
| AD, RDW, SDW, TPB | 40442312 | 1, 4 | 1 | Chr09 | 7.10E-06 | 5.15 | 0.306 | C/A | C:131_A:7 | 0.05 |
| RDW | 40958088 | 1, 4, 5 | 2,3 | Chr04 | 9.7E-05 | 4.01 | 0.264 | A/G | A:117_G:7 | 0.06 |
| SA | 42374764 | 4 | 2,3 | Chr20 | 6.1E-05 | 4.22 | 0.270 | G/T | G:124_T:8 | 0.06 |
| SA | 42374776 | 4 | 2,3 | Chr20 | 7.2E-05 | 4.14 | 0.250 | A/T | A:124_T:8 | 0.06 |
| SA | 42374808 | 4 | 2,3 | Chr20 | 7.2E-05 | 4.14 | 0.250 | T/C | T:124_C:8 | 0.06 |
| RV | 45819633 | 4, 5 | 2,3 | Chr20 | 7E-05 | 4.16 | 0.251 | A/G | A:105_G:23 | 0.18 |
SL = shoot length, SDW = shoot dry weight, RDW = root dry weight, TRL = total root length, AD = average diameter, RDW/SDW = root dry weight per shoot dry weight, TPB = total plant biomass, RV = root volume, SA = surface area, BN = branching number, a method 1–5 refers to GLM, MLM, CMLM, FaST-LMM, and EMMAX, respectively, b stage 1–3 refers to VC, V1, and V2, respectively, MAF = minor allele frequency, R2 = phenotypic contribution, Chr = chromosome.