Table 2.
Candidate genes, chromosomal position and SNPs significantly associated with Area under Disease Progress Curve (AUDPC) detected by SNP-based GWAS
| No. | Candidate gene | Chromosome | Physical position (AGP v.2) | SNP | Allele | P value | FDR* | MAFa | R2 | Annotation |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Intergenic | 3 | 103166745 | PZE-103062307 | A,G | 2.67E-06 | 0.031 | 0.09 | 0.02 | |
| 2 | Intergenic | 3 | 103544700 | PZE-103062210 | A,G | 1.88E-05 | 0.074 | 0.17 | 0.02 | |
| 3 | Intergenic | 3 | 103769943 | PZE-103062159 | A,C | 9.87E-06 | 0.074 | 0.13 | 0.02 | |
| 4 | GRMZM2G171605 | 4 | 186590896 | PZE-104110312 | A,G | 1.74E-07 | 0.004 | 0.18 | 0.03 | 4'phosphopante theinyl transferase |
| 5 | GRMZM2G005308 | 6 | 160053330 | PZE-106113397 | A,G | 1.96E-05 | 0.074 | 0.24 | 0.02 | U3 small nucleolar ribonucleoprotein |
| 6 | GRMZM2G151651 | 7 | 33447828 | SYNGENTA5726 | G,A | 4.58E-08 | 0.002 | 0.08 | 0.03 | |
| 7 | GRMZM2G100107 | 7 | 91683817 | SYN16533 | G,A | 2.07E-05 | 0.074 | 0.44 | 0.02 | SANT associated |
| 8 | GRMZM2G100107 | 7 | 91684720 | PZE-107044973 | A,G | 1.74E-05 | 0.074 | 0.43 | 0.02 | SANT associated |
| 9 | Intergenic | 7 | 91686972 | PZE-107044977 | C,A | 1.43E-05 | 0.074 | 0.44 | 0.02 | |
| 10 | Intergenic | 7 | 92335869 | PZE-107045210 | G,A | 3.64E-06 | 0.034 | 0.21 | 0.02 | |
| 11 | Intergenic | 8 | 37657703 | PZE-108032335 | G,A | 1.43E-05 | 0.074 | 0.36 | 0.02 | |
| 12 | GRMZM2G158141 | 10 | 91956279 | PZE-110049068 | G,A | 1.28E-05 | 0.074 | 0.09 | 0.02 | Antifreeze protein |
*False discovery rate-corrected p-values
aMinor allele frequency