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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    
  1. % r 2 is the proportion of the phenotypic variance explained by the SNP for the association mapping population.