Table 4.
List of significant SNPs associated with agronomic traits evaluated in four environments under artificial inoculation of Cercospora zeina.
| SNP | Chr | Position (bp) | Bin name | MLM-P value | MAF | Effect |
|---|---|---|---|---|---|---|
| Anthesis date | ||||||
| DT3_1407684 | 3 | 1407684 | 3.01 | 2.03 × 10−6 | 0.34 | −0.72 |
| DT3_28537024 | 3 | 28537024 | 3.04 | 1.25 × 10−4 | 0.05 | −1.51 |
| DT3_159134665 | 3 | 159134665 | 3.05 | 1.33 × 10−4 | 0.06 | −1.25 |
| DT3_173798390 | 3 | 173798390 | 3.06 | 2.39 × 10−5 | 0.35 | −0.74 |
| DT5_4115653 | 5 | 4115653 | 5.01 | 2.18 × 10−6 | 0.15 | 1.04 |
| DT5_80046482 | 5 | 80046482 | 5.03 | 5.09 × 10−6 | 0.30 | 1.21 |
| DT5_190321766 | 5 | 190321766 | 5.05 | 1.18 × 10−5 | 0.35 | −0.70 |
| DT6_114255122 | 6 | 114255122 | 6.04 | 7.73 × 10−9 | 0.21 | 1.18 |
| DT6_146530203 | 6 | 146530203 | 6.05 | 1.68 × 10−5 | 0.30 | 0.71 |
| DT7_168724486 | 7 | 168724486 | 7.05 | 2.92 × 10−8 | 0.35 | −1.00 |
| DT8_148947397 | 8 | 148947397 | 8.06 | 1.14 × 10−8 | 0.11 | −1.43 |
| DT9_76104516 | 9 | 76104516 | 9.03 | 1.16 × 10−10 | 0.06 | −2.45 |
| DT9_116598435 | 9 | 116598435 | 9.04 | 1.88 × 10−4 | 0.42 | 0.64 |
| Silking date | ||||||
| DT1_36755457 | 1 | 36755457 | 1.03 | 9.22 × 10−5 | 0.16 | −0.76 |
| DT1_160031116 | 1 | 160031116 | 1.05 | 3.41 × 10−5 | 0.29 | −0.76 |
| DT1_196931772 | 1 | 196931772 | 1.06 | 2.47 × 10−5 | 0.22 | −0.84 |
| DT2_215851764 | 2 | 215851764 | 2.08 | 2.22 × 10−6 | 0.07 | −1.31 |
| DT3_1469626 | 3 | 1469626 | 3.01 | 6.50 × 10−5 | 0.50 | 0.61 |
| DT3_9577871 | 3 | 9577871 | 3.03 | 8.45 × 10−7 | 0.44 | −0.82 |
| DT3_132334454 | 3 | 132334454 | 3.05 | 3.16 × 10−6 | 0.07 | −1.38 |
| DT4_208901175 | 4 | 208901175 | 4.09 | 1.29 × 10−4 | 0.06 | −1.22 |
| DT5_217466828 | 5 | 217466828 | 5.09 | 5.50 × 10−11 | 0.16 | −1.47 |
| DT6_85907826 | 6 | 85907826 | 6.01 | 6.26 × 10−5 | 0.06 | 1.65 |
| DT7_54538519 | 7 | 54538519 | 7.02 | 2.60 × 10−5 | 0.49 | −0.61 |
| DT7_174089319 | 7 | 174089319 | 7.05 | 1.95 × 10−4 | 0.13 | −0.78 |
| DT8_63984569 | 8 | 63984569 | 8.03 | 3.34 × 10−5 | 0.15 | −0.93 |
| DT9_76308336 | 9 | 76308336 | 9.03 | 4.59 × 10−6 | 0.08 | −1.89 |
| Anthesis-Silking interval | ||||||
| DT5_216421061 | 5 | 216421061 | 5.09 | 2.09 × 10−4 | 0.21 | 0.71 |
| DT7_7541489 | 7 | 7541489 | 7.01 | 3.02 × 10 − 4 | 0.05 | 1.18 |
| Plant height | ||||||
| DT2_11667280 | 2 | 11667280 | 2.02 | 1.28 × 10−4 | 0.14 | 7.93 |
| DT2_27642609 | 2 | 27642609 | 2.03 | 1.45 × 10−4 | 0.39 | 5.16 |
| DT2_27774525 | 2 | 27774525 | 2.03 | 1.40 × 10−4 | 0.41 | 5.11 |
| DT6_168920192 | 6 | 168920192 | 6.08 | 3.31 × 10−5 | 0.06 | −12.44 |
| DT8_122249319 | 8 | 122249319 | 8.04 | 1.69 × 10−4 | 0.09 | −8.72 |
| DT8_138595600 | 8 | 138595600 | 8.05 | 2.14 × 10−4 | 0.18 | −6.60 |
| DT10_56267943 | 10 | 56267943 | 10.03 | 6.73 × 10−5 | 0.05 | 11.87 |
| DT10_101212899 | 10 | 101212899 | 10.04 | 8.59 × 10−5 | 0.05 | −11.54 |
| DT10_101212965 | 10 | 101212965 | 10.04 | 7.99 × 10−5 | 0.06 | 10.78 |
| DT10_101213049 | 10 | 101213049 | 10.04 | 1.97 × 10−5 | 0.07 | 10.99 |
| DT10_124620967 | 10 | 124620967 | 10.04 | 1.99 × 10−4 | 0.10 | −8.19 |
| Ear height | ||||||
| DT5_215513759 | 5 | 215513759 | 5.08 | 3.32 × 10−5 | 0.12 | −5.54 |
| DT7_5660772 | 7 | 5660772 | 7.01 | 1.61 × 10−4 | 0.14 | 4.76 |
| DT9_127735255 | 9 | 127735255 | 9.05 | 6.61 × 10−5 | 0.21 | 4.21 |
| DT10_101212899 | 10 | 101212899 | 10.04 | 2.20 × 10−4 | 0.05 | −7.02 |
| DT10_101212965 | 10 | 101212965 | 10.04 | 4.18 × 10−5 | 0.06 | 7.18 |
| DT10_101213049 | 10 | 101213049 | 10.04 | 7.69 × 10−5 | 0.07 | 6.60 |
MAF, minor allele frequency, effect = allele effect; MLM P-value = probability value for the mixed linear model; GLS, disease severity, and AUDPC, area under disease progress curve values under artificial inoculation of GLS conditions; position = the physical position of the SNP (Ref Gen_v3 of B73).