TABLE 7.
Details of the significant SNPs associated with ASI, Pht, Eht, EPO, EPP, and SEN under optimum and low N managements using the FarmCPU model with a Bonferroni threshold of P < 0.05.
| Trait | SNP | Chr. | Position | P-value | MAF | Effect |
| ASI_Opt | S1_274946693 | 1 | 274946693 | 2.08E-07 | 0.08 | –0.21 |
| S2_6636633 | 2 | 6636633 | 4.99E-09 | 0.17 | 0.17 | |
| S2_54204647 | 2 | 54204647 | 2.82E-08 | 0.44 | 0.11 | |
| S3_128687310 | 3 | 128687310 | 8.68E-10 | 0.33 | 0.16 | |
| S4_235073935 | 4 | 235073935 | 4.22E-08 | 0.06 | 0.22 | |
| S5_195672028 | 5 | 195672028 | 4.59E-14 | 0.07 | 0.37 | |
| S7_24409023 | 7 | 24409023 | 3.88E-12 | 0.25 | 0.18 | |
| S7_155590511 | 7 | 155590511 | 8.19E-08 | 0.22 | 0.12 | |
| S8_136094451 | 8 | 136094451 | 5.01E-10 | 0.26 | –0.14 | |
| S9_118046290 | 9 | 118046290 | 7.10E-08 | 0.22 | 0.13 | |
| S10_33353122 | 10 | 33353122 | 2.32E-09 | 0.16 | –0.20 | |
| ASI_LowN | S1_5810155 | 1 | 5810155 | 3.93E-08 | 0.19 | 0.17 |
| S2_226325975 | 2 | 226325975 | 1.54E-07 | 0.29 | –0.15 | |
| S3_32033690 | 3 | 32033690 | 1.58E-07 | 0.49 | 0.13 | |
| S3_147401613 | 3 | 147401613 | 1.06E-08 | 0.43 | –10.15 | |
| S4_37297564 | 4 | 37297564 | 1.68E-07 | 0.22 | –0.16 | |
| S6_164497574 | 6 | 164497574 | 9.27E-09 | 0.27 | 0.16 | |
| S10_4586049 | 10 | 4586049 | 6.45E-09 | 0.48 | –0.16 | |
| Pht_Opt | S3_64819581 | 3 | 64819581 | 1.62E-07 | 0.06 | 3.46 |
| S4_46166070 | 4 | 46166070 | 7.98E-08 | 0.37 | –1.69 | |
| S4_184955101 | 4 | 184955101 | 3.98E-08 | 0.25 | 2.10 | |
| S7_6297685 | 7 | 6297685 | 5.22E-12 | 0.26 | –2.77 | |
| S10_143502717 | 10 | 143502717 | 1.61E-07 | 0.16 | 2.19 | |
| Pht_LowN | S1_17679579 | 1 | 17679579 | 4.65E-08 | 0.10 | 2.32 |
| S3_199254673 | 3 | 199254673 | 1.88E-13 | 0.21 | –3.54 | |
| S4_237693358 | 4 | 237693358 | 2.59E-07 | 0.12 | 2.50 | |
| S8_25351243 | 8 | 25351243 | 1.05E-07 | 0.32 | –1.48 | |
| Eht_Opt | S2_140662928 | 2 | 140662928 | 2.44E-07 | 0.27 | –1.71 |
| S8_158098622 | 8 | 158098622 | 7.18E-09 | 0.37 | 1.75 | |
| Eht_LowN | S1_16698847 | 1 | 16698847 | 2.94E-12 | 0.12 | –2.55 |
| S1_199339693 | 1 | 199339693 | 1.60E-08 | 0.06 | 1.92 | |
| S1_274946693 | 1 | 274946693 | 3.84E-09 | 0.08 | –2.31 | |
| S2_196870448 | 2 | 196870448 | 1.54E-08 | 0.11 | 1.63 | |
| S3_217796834 | 3 | 217796834 | 7.05E-08 | 0.15 | 1.37 | |
| S5_83133270 | 5 | 83133270 | 5.66E-10 | 0.06 | 2.60 | |
| S6_7046560 | 6 | 7046560 | 4.63E-09 | 0.24 | –1.26 | |
| S7_40379325 | 7 | 40379325 | 4.01E-08 | 0.21 | 1.23 | |
| S10_126687226 | 10 | 126687226 | 1.81E-10 | 0.07 | 2.24 | |
| S10_145097517 | 10 | 145097517 | 2.10E-08 | 0.33 | 1.17 | |
| EPO_Opt | S1_71065792 | 1 | 71065792 | 1.76E-07 | 0.07 | 0.01 |
| S6_97945994 | 6 | 97945994 | 1.47E-08 | 0.09 | 0.01 | |
| S8_72067641 | 8 | 72067641 | 2.88E-09 | 0.37 | 0.00 | |
| S10_143712477 | 10 | 143712477 | 2.71E-08 | 0.08 | 0.01 | |
| EPO_LowN | S1_207055175 | 1 | 207055175 | 1.37E-07 | 0.22 | 0.00 |
| S1_274946693 | 1 | 274946693 | 3.01E-09 | 0.08 | –0.01 | |
| S1_285229689 | 1 | 285229689 | 2.52E-10 | 0.42 | –0.01 | |
| S2_33350339 | 2 | 33350339 | 8.02E-10 | 0.33 | 0.00 | |
| S6_97945994 | 6 | 97945994 | 4.75E-11 | 0.09 | 0.01 | |
| S10_123956017 | 10 | 123956017 | 6.75E-09 | 0.13 | 0.01 | |
| EPP_LowN | S1_122756821 | 1 | 122756821 | 2.54E-08 | 0.47 | –0.01 |
| S4_174009677 | 4 | 174009677 | 1.17E-07 | 0.07 | –0.02 | |
| S5_188825516 | 5 | 188825516 | 1.01E-07 | 0.18 | –0.01 | |
| S10_148304779 | 10 | 148304779 | 1.33E-07 | 0.31 | 0.01 | |
| SEN_Opt | S1_220067760 | 1 | 220067760 | 3.46E-09 | 0.47 | –0.08 |
| S4_177150249 | 4 | 177150249 | 1.53E-08 | 0.19 | 0.10 | |
| S5_8351127 | 5 | 8351127 | 1.02E-07 | 0.45 | –0.08 | |
| S8_159648136 | 8 | 159648136 | 2.12E-07 | 0.24 | –0.08 | |
| S9_153449703 | 9 | 153449703 | 1.70E-08 | 0.47 | –0.08 |
Where MAF is the Minor Allele Frequency, effect is the Allele Effect, and P-value is for the mixed linear model’ ASI, anthesis-silking interval; PH, plant height; EH, ear height; EPO, ear position; EPP, ears per plant; and SEN, senescence under optimum (Opt), and low N stress (Low N) conditions.