Table 1. Candidate Al tolerance genes evaluated by association mapping.
| Gene ID | Gene Name | MAGI ref seq# | Length (bp) | Lines (#) | Sites (#) | Chr (#) | ctg (#) | BIN (#) |
| ME | Malic Enzyme | 3.1_47445 | 626 | 255 | 12 | 6 | 282 | 6.05 |
| FE | Iron-responsive transporter-like | 3.1_61976 | 503 | 240 | 11 | 2 | 106 | 2.08 |
| ANTI | Major facilitator superfamily antiporter | 3.1_69188 | 549 | 246 | 14 | 6 | 285 | 6.05 |
| ABC | ABC transporter-like protein | 3.1_80359 | 373 | 251 | 21 | 2 | 106 | 2.08 |
| ISL | Isocitrate Lyase | 3.1_108586 | 526 | 228 | 6 | 7 | 322 | 7.03 |
| AUX1 | Amino acid permease AUX1 | 3.1_112316 | 526 | 206 | 23 | 2 | 106 | 2.08 |
| SAHH | SAH hydrolase | 4.0_116767 | 500 | 206 | 6 | 4 | 160 | 4.03 |
| P450 | Cytochrome P450 | 4.0_145633 | 786 | 246 | 14 | 3 | 138 | 3.06 |
| PME | Pectin methylesterase | 4.0_158804 | 454 | 270 | 3 | 1 | 49 | 1.08 |
| PI3K | Phosphatidylinositol 3-kinase | 4.0_112182 | 590 | 254 | 10 | 4 | 172 | 4.05 |
| OO2 | Germin2 (oxalate oxidase) | 4.0_67335 | 729 | 182 | 26 | 10 | 399 | 10.03 |
| IDH | Isocitrate dehydrogenase | 4.0_48631 | 1061 | 253 | 14 | 4 | 173 | 4.05 |
| FUM | Fumerase | 4.0_35824 | 646 | 269 | 8 | 1 | 14 | 1.04 |
| AL1 | ZmALMT1 | 3.1_92675 | 476 | 182 | 31 | 10 | 412 | 10.04 |
| AL2 | ZmALMT2 | 3.1_93496 | 487 | 199 | 17 | 10 | 412 | 10.04 |
| AL3 | ZmALMT3 | 3.1_92049 | 633 | 193 | 9 | 5 | 252 | 5.07 |
| AL5 | ZmALMT5 | 3.1_811363 | 743 | 215 | 24 | 10 | 412 | 10.044 |
| AL8 | ZmALMT8 | 3.1_90876 | 504 | 208 | 26 | 5 | 247 | 5.06 |
| AL9 | ZmALMT9 | 3.1_6591 | 288 | 263 | 2 | 5 | 214 | 5.03 |
| AL16 | ZmALMT16 | 3.1_36360 | HAP* | 285 | 1 | 10 | 415 | 10.06 |
| ASL | ZmASL (region 1) | 3.1_41691 | 1179 | 278 | 32 | 1 | 9 | 1.02 |
| ASL | ZmASL (region 2) | 3.1_41691 | 715 | 240 | 21 | 1 | 9 | 1.02 |
Thirteen genes were selected from gene expression analysis, while another eight came from comparative genomics. Genes were identified from genome survey sequence contigs created by the MAGI Project. MAGI build version and reference number are reported. “Length” describes the total length of sequence used for polymorphic site identification. “# Lines” refers to the number of entries with sufficient information to include in the association analysis. “# Sites” refers to polymorphisms that occurred at greater than 10% frequency. Physical-genetic map locations for each candidate gene are reported according to chromosome, genomic sequencing contig and genetic map bin. Genetic bins that appear in bold represent those under previously reported Al tolerance QTL. Gene AL16 was evaluated by a large indel (*HAP) rather than by gene sequence. Gene ASL underwent two rounds of sequence analysis.