Table 3.
The significant single nucleotide polymorphisms (SNPs) and their candidate genes associated with plant height (PH) and ear height (EH) identified in this study.
| Trait | SNP | Chr | Positiona | P-value | R2 | Candidate gene | Annotation |
|---|---|---|---|---|---|---|---|
| PH | S2_178613725 | 2 | 178613725 | 8.18E-05 | 0.064 | GRMZM2G116196 | Unknown |
| S2_178613733 | 2 | 178613733 | 9.82E-05 | 0.062 | |||
| S2_204259050 | 2 | 204259050 | 6.38E-05 | 0.074 | – | – | |
| S2_204259051 | 2 | 204259051 | 6.38E-05 | 0.074 | |||
| S2_204259052 | 2 | 204259052 | 6.38E-05 | 0.074 | |||
| S2_204259054 | 2 | 204259054 | 6.38E-05 | 0.074 | |||
| S3_18231963 | 3 | 18231963 | 3.59E-06 | 0.093 | GRMZM5G836162 | Mitochondrial substrate carrier family protein | |
| S3_18232028 | 3 | 18232028 | 2.82E-05 | 0.076 | |||
| S3_18232030 | 3 | 18232030 | 2.37E-05 | 0.079 | |||
| S3_20426411 | 3 | 20426411 | 8.37E-05 | 0.077 | GRMZM2G437100 | HSP20-like chaperones superfamily protein | |
| S3_49619525 | 3 | 49619525 | 4.99E-05 | 0.070 | GRMZM2G322186 | Pyridoxal phosphate-dependent transferase superfamily protein | |
| S3_49619564 | 3 | 49619564 | 2.41E-05 | 0.076 | |||
| S3_49619609 | 3 | 49619609 | 8.91E-05 | 0.063 | |||
| S3_138737914 | 3 | 138737914 | 6.82E-05 | 0.083 | |||
| S3_138737941 | 3 | 138737941 | 6.82E-05 | 0.083 | – | – | |
| S3_138737949 | 3 | 138737949 | 6.82E-05 | 0.083 | |||
| S5_26139412 | 5 | 26139412 | 9.06E-05 | 0.073 | – | – | |
| S6_124299082 | 6 | 124299082 | 3.36E-06 | 0.093 | GRMZM2G402538 | Acyltransferase with RING/FYVE/PHD-type zinc finger protein | |
| S6_124300076 | 6 | 124300076 | 4.17E-05 | 0.077 | |||
| S6_124841703 | 6 | 124841703 | 8.29E-05 | 0.072 | – | – | |
| S6_164148781 | 6 | 164148781 | 5.25E-05 | 0.071 | GRMZM2G079583 | Leucine-rich repeat protein kinase family protein | |
| EH | S2_25387853 | 2 | 25387853 | 6.48E-05 | 0.062 | GRMZM2G031360 | Clathrin adaptor complexes medium subunit family protein |
| S2_67260246 | 2 | 67260246 | 3.94E-05 | 0.075 | – | – | |
| S2_195056557 | 2 | 195056557 | 5.99E-05 | 0.075 | GRMZM2G034113 | Homeobox associated leucine zipper | |
| S3_1976523 | 3 | 1976523 | 4.61E-06 | 0.088 | GRMZM2G083749 | Helix-loop-helix (bHLH) DNA-binding superfamily protein | |
| S3_1976526 | 3 | 1976526 | 4.61E-06 | 0.088 | |||
| S3_2084297 | 3 | 2084297 | 3.01E-05 | 0.078 | GRMZM2G153181 | RNA polymerase I-associated factor PAF67 | |
| S3_58714371 | 3 | 58714371 | 4.47E-05 | 0.068 | GRMZM2G378547 | Protein kinase superfamily protein | |
| S3_89609331 | 3 | 89609331 | 8.82E-05 | 0.063 | GRMZM2G503156 | AGC (cAMP-dependent, cGMP-dependent and protein kinase C) kinase family protein | |
| S4_74268672 | 4 | 74268672 | 5.64E-05 | 0.066 | GRMZM2G091503 | Signal recognition particle binding | |
| S4_130433483 | 4 | 130433483 | 6.56E-05 | 0.062 | GRMZM2G127924 | Phototropic-responsive NPH3 family protein | |
| S4_130433496 | 4 | 130433496 | 6.39E-05 | 0.062 | |||
| S5_69308290 | 5 | 69308290 | 7.01E-05 | 0.064 | GRMZM2G389155 | Transducin/WD40 repeat-like superfamily protein | |
| S6_113668398 | 6 | 113668398 | 1.95E-05 | 0.073 | AC202439.3_FG006 | Sodium symporters; urea transmembrane transporters | |
| S6_132980291 | 6 | 132980291 | 3.46E-05 | 0.079 | – | – | |
| S6_137828752 | 6 | 137828752 | 1.66E-05 | 0.079 | GRMZM2G170365 | RNA-binding (RRM/RBD/RNP motifs) family protein | |
| S6_139882410 | 6 | 139882410 | 9.22E-05 | 0.069 | GRMZM2G113156 | SMAD/FHA domain-containing protein | |
| S9_117399420 | 9 | 117399420 | 1.82E-05 | 0.078 | GRMZM5G861756 | Multimeric translocon complex in the outer envelope membrane | |
| S9_117399428 | 9 | 117399428 | 1.82E-05 | 0.078 | |||
| S9_117399471 | 9 | 117399471 | 2.18E-05 | 0.078 | |||
| S9_117618087 | 9 | 117618087 | 1.16E-05 | 0.095 | – | – |
a
Position indicates the physical position of B73 RefGen_v2.