Table 2.
Significantly associated single-nucleotide polymorphisms (SNPs) along with the predicted gene model and their function detected by genome-wide association studies in CIMMYT association mapping panel for charcoal rot resistance.
| Marker | Ch | P-Value | PVE% | Favorable allele | Predicted gene model | Gene name/best matching ortholog | Plants | Reported function | References |
|---|---|---|---|---|---|---|---|---|---|
| S5_48504604 | 5 | 5.88 × 10−06 | 5.63 | G | – | – | – | – | |
| S10_117560618 | 10 | 1.12 × 10−05 | 5.3 | A | GRMZM2G072513 | OSJNBa0088K19.7-like protein | Rice | – | |
| S10_144684808 | 10 | 1.29 × 10−05 | 5.22 | G | GRMZM2G136895 | Zea mays Beta-D-xylosidase 4 | Arabidopsis, other plants | Cell wall modification, fruit development | Itai et al., 2003; Minic et al., 2004; Liao et al., 2012 |
| S9_1994787 | 9 | 1.44 × 10−05 | 5.17 | G | GRMZM2G500051 | – | – | – | |
| S8_165726556 | 8 | 1.68 × 10−05 | 5.09 | C | GRMZM2G414696 | – | – | – | |
| S10_115937334 | 10 | 1.97 × 10−05 | 5.01 | A | GRMZM2G050647 | Exocyst complex component SEC5 | Arabidopsis, other plants | Plant-pathogen interaction | Du et al., 2018 |
| S5_19528704 | 5 | 2.11 × 10−05 | 4.97 | G | GRMZM2G178767 | Zea mays Dof zinc-finger protein DOF5.7 | Plants | Abiotic stress, biotic stress | Sakamoto et al., 2004; Guo et al., 2009 |
| S5_19528705 | 5 | 2.19 × 10−05 | 4.95 | A | |||||
| S4_167190764 | 4 | 2.37 × 10−05 | 4.92 | A | GRMZM2G168337 | Zea mays Nicastrin | Arabidopsis, maize | Promotes maturation and proper trafficking of complex components and substrate recognition, biotic stress | Wang et al., 2012; Smolarkiewicz et al., 2014 |
| S8_165726551 | 8 | 2.38 × 10−05 | 4.91 | C | GRMZM2G414696 | – | – | – | – |
| S1_52605386 | 1 | 2.85 × 10−05 | 4.82 | T | – | – | – | – | – |
| S1_200489143 | 1 | 2.90 × 10−05 | 4.81 | T | GRMZM2G557453 | – | – | – | – |
| S6_163106367 | 6 | 3.07 × 10−05 | 4.78 | A | AC206312.3_FGT008 | – | – | – | – |
| S8_165726574 | 8 | 3.98 × 10−05 | 4.65 | A | GRMZM2G414696 | – | – | – | – |
| S3_2125663 | 3 | 4.31 × 10−05 | 4.61 | T | GRMZM2G170047 | Zea mays Cytochrome P450 71A26 | Maize, wheat, barley | Oxidation- reduction reaction, defense mechanism, secondary metabolite synthesis, Fusarium head blight | Morant et al., 2003; Irmisch et al., 2015; Gunupuru et al., 2018 |
| S7_156114994 | 7 | 4.34 × 10−05 | 4.61 | G | GRMZM2G465999 | Zea mays G-type lectin S-receptor-like serine/threonine-protein kinase B120 | Plants | Biotic and abiotic stress tolerance, plant defense | Lannoo and Van Damme, 2014 |
| S6_103513378 | 6 | 4.62 × 10−05 | 4.57 | C | GRMZM2G122172 | Aldehyde dehydrogenase family 2 member C4 | Plants | Abiotic and biotic stresses tolerance | Wen et al., 2012; Brocker et al., 2013 |
| S6_103513337 | 6 | 4.73 × 10−05 | 4.56 | A | |||||
| S8_165726553 | 8 | 4.80 × 10−05 | 4.55 | A | GRMZM2G414696 | – | – | – |
Ch, chromosome, PVE, Phenotypic varinace explained.