Table 3 Single nucleotide polymorphism (SNP) markers significantly (FDR = 0.05) associated with traits evaluated under Fe-deficient and the Fe-sufficient iron regime
From: Genome-wide association mapping of iron homeostasis in the maize association population
Marker | Position | Allele | Effect | Best hit | Confirmed | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Fe regime | Trait | locus | Chr. | (bp) | P -value | 1/2 | Allele 1-2 | % r 2 | Gene | UniProt ID | Annotation |
Deficient | NEC | S1_276695950 | 1 | 276,695,950 | 7.0e-07 | G/A | 0.91 | 10.58 | |||
S2_3229998 | 2 | 3,229,998 | 9.4e-08 | T/A | 1.51 | 12.39 | GRMZM2G018692 | Q56UD0 | Beta-fructofuranosidase, insoluble isoenzyme 6 | ||
S2_28932171 | 2 | 28,932,171 | 4.4e-08 | A/T | 1.55 | 13.03 | |||||
S2_111136826 | 2 | 111,136,826 | 1.5e-06 | A/G | 1.16 | 10.08 | |||||
S2_186894397 | 2 | 186,894,397 | 9.0e-07 | C/T | 0.81 | 10.63 | GRMZM2G168163 | Q9SX79 | Polyadenylate-binding protein RBP47C | ||
S3_1772101 | 3 | 1,772,101 | 7.4e-07 | A/G | 0.83 | 10.89 | |||||
S5_23763641 | 5 | 23763641 | 1.4e-06 | C/G | 1.04 | 10.50 | GRMZM2G376743 | Q04980 | Low-temperature-induced 65 kDa protein | ||
S5_48571692 | 5 | 48,571,692 | 1.5e-09 | T/C | 1.16 | 14.68 | GRMZM5G848124 | Q851X4 | Expressed protein | ||
S5_168028100 | 5 | 168,028,100 | 1.1e-06 | C/G | 1.34 | 10.08 | |||||
S5_174017789 | 5 | 174,017,789 | 1.6e-07 | C/T | 0.89 | 11.09 | GRMZM2G460958 | Q9LRB7 | E3 ubiquitin-protein ligase EL5 | ||
S5_175221001 | 5 | 175,221,001 | 1.2e-07 | T/G | 1.28 | 11.52 | GRMZM2G128029 | Q2R2T4 | CASP-like protein Os11g0549625 | ||
S7_106685037 | 7 | 106,685,037 | 1.0e-06 | T/G | 1.21 | 10.05 | |||||
Simultaneous fit | 30.78 | ||||||||||
RW | S4_167072278 | 4 | 167,072,278 | 3.7e-10 | C/A | -6.23 | 18.81 | GRMZM2G015049 | Q9LR00 | SAUR-like auxin-responsive protein | |
S6_160330734 | 6 | 160,330,734 | 1.5e-07 | C/G | -3.67 | 13.63 | |||||
S6_164144405 | 6 | 164,144,405 | 6.0e-07 | T/C | -4.78 | 12.73 | GRMZM2G377613 | P23923 | Transcription factor HBP-1b(c38) | ||
S7_173225158 | 7 | 173,225,158 | 4.4e-07 | G/T | -4.31 | 13.69 | GRMZM2G381386 | F4II36 | RING-finger, DEAD-like helicase, PHD and SNF2 domain | ||
Simultaneous fit | 34.65 | ||||||||||
SDW | S9_28406038 | 9 | 28,406,038 | 7.0e-10 | C/T | -0.72 | 16.35 | ||||
S9_29869940 | 9 | 29,869,940 | 1.7e-07 | T/C | -0.62 | 11.44 | |||||
Simultaneous fit | 13.01 | ||||||||||
Sufficient | H 2O | S1_43769442 | 1 | 43,769,442 | 1.6e-06 | A/G | 3.00 | 13.52 | |||
S10_5846137 | 10 | 5,846,137 | 5.4e-07 | C/A | 3.59 | 14.81 | |||||
S2_209283962 | 2 | 209,283,962 | 1.4e-06 | G/T | 2.27 | 14.06 | |||||
S2_220878478 | 2 | 220,878,478 | 4.7e-08 | C/T | 2.99 | 16.30 | |||||
S3_28612747 | 3 | 28,612,747 | 7.7e-07 | T/C | 2.75 | 14.90 | |||||
S4_230588662 | 4 | 230,588,662 | 1.2e-06 | G/A | 1.91 | 14.11 | GRMZM2G038588 | Q54N48 | Protein CLP1 homolog | ||
S5_60131644 | 5 | 60,131,644 | 1.3e-06 | A/T | 2.38 | 13.80 | GRMZM2G097683 | Q9XGX0 | Putative zinc finger protein SHI | ||
S6_131544420 | 6 | 131,544,420 | 8.4e-12 | T/C | 5.04 | 21.21 | |||||
S6_164852452 | 6 | 164,852,452 | 7.2e-07 | G/A | -0.10 | 0.16 | GRMZM2G030305 | Q5SN53 | Mitogen-activated protein kinase 8 | ||
Simultaneous fit | 57.47 | ||||||||||
RW | S1_46679288 | 1 | 46,679,288 | 3.3e-09 | C/G | -12.59 | 20.69 | GRMZM2G455809 | P50160 | Sex determination protein tasselseed-2 | |
S1_80919352 | 1 | 80,919,352 | 6.4e-08 | A/C | -9.18 | 17.60 | GRMZM2G087878 | ||||
S1_82391496 | 1 | 82,391,496 | 2.5e-10 | G/A | -12.76 | 20.72 | |||||
S6_88996310 | 6 | 88,996,310 | 6.7e-07 | C/T | -7.87 | 15.38 | GRMZM2G439598 | ||||
S7_108322405 | 7 | 108,322,405 | 1.8e-06 | T/C | 0.58 | 0.15 | |||||
S9_42004118 | 9 | 42,004,118 | 9.8e-07 | G/A | 0.63 | 0.86 | |||||
S9_49309187 | 9 | 49,309,187 | 5.4e-07 | C/G | -9.48 | 15.71 | GRMZM2G040605 | ||||
Simultaneous fit | 38.93 | ||||||||||
SP3 | S5_25511041 | 5 | 25,511,041 | 7.9e-08 | A/C | -4.41 | 10.99 | GRMZM2G305446 | Q9ATL7 | Aquaporin TIP3-1 | |
Simultaneous fit | 10.99 |