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Table 2 Single nucleotide polymorphism (SNP) markers significantly (FDR = 0.05) associated in the association mapping population which were located within confidence intervals of QTL detected for the same trait in the IBM population [ 12 ]

From: Genome-wide association mapping of iron homeostasis in the maize association population

    Marker   Position Interval   Allele Effect    Best hit Confirmed
Fe regime Trait QTL locus Chr. (bp) (cM) P -value 1/2 Allele 1-2 % r 2 Gene UniProt ID Annotation
Deficient NEC QTL1 S1_28643309 1 28,643,309 205.0 - 208.5 8.2e-05 G/A 0.43 6.04 GRMZM2G040828 Q9LVS3 Pentatricopeptide repeat-containing protein At5g47360
    S1_28643428 1 28,643,428 205.0 - 208.5 1.7e-04 G/A 0.41 5.43 GRMZM2G040828 Q9LVS3 Pentatricopeptide repeat-containing protein At5g47360
    S1_28765554 1 28,765,554 205.0 - 208.5 1.7e-04 A/G 0.42 5.51 GRMZM2G036257 O81117 Cytochrome P450 94A1
    S1_28765627 1 28,765,627 205.0 - 208.5 1.5e-04 G/A 0.39 4.96 GRMZM2G036257 O81117 Cytochrome P450 94A1
    Simultaneous fit        5.29    
  RW QTL3 S5_3733903 5 3,733,903 73.3 - 74.4 2.1e-04 C/T -3.87 8.47 GRMZM2G701295   
            GRMZM2G350471 Q75HK3 Expressed protein
    S5_3783037 5 3,783,037 73.3 - 74.4 1.2e-03 C/G 0.60 0.18 GRMZM2G350428 Q6AV48 CLE family OsCLE305 protein
    Simultaneous fit        8.67    
  RW QTL4 S5_180440433 5 180,440,433 410.8 - 413.6 3.0e-04 C/G 0.27 0.04    
    S5_181192685 5 181,192,685 410.8 - 413.6 2.3e-04 T/C 0.24 0.03 AC205703.4_FG005 Q8GUM4 Uncharacterized membrane protein At3g27390
    Simultaneous fit        0.39    
  SDW/SL QTL1 S8_165976755 8 165,976,755 464.0 - 466.5 6.0e-05 C/T -7.09 6.87 GRMZM2G148773   
    Simultaneous fit        6.87    
  SP3 QTL8 S9_26961652 9 26,961,652 220.7 - 223.9 5.7e-06 A/T 5.85 7.92 GRMZM2G156218 F4K975 Sec14p-like phosphatidylinositol transfer family protein
    S9_37654085 9 37,654,085 220.7 - 223.9 1.4e-04 C/T 6.16 5.56    
    S9_45093751 9 45,093,751 220.7 - 223.9 4.6e-05 A/G 4.20 6.78 GRMZM2G177084 Q9FG31 Late embryogenesis abundant protein 4-5
    Simultaneous fit        11.45    
  SP6 QTL3 S1_256662971 1 256,662,971 825.8 - 833.0 1.2e-04 G/A 9.88 5.82    
    Simultaneous fit        5.82    
Sufficient SP4 QTL1 S1_256466020 1 256,466,020 833.0 - 839.3 7.8e-05 T/C 3.66 6.32    
    S1_257972883 1 257,972,883 833.0 - 839.3 1.1e-04 T/A 5.45 6.05 GRMZM2G055037 Q3E8H0 S-ribonuclease binding protein
    Simultaneous fit        10.31    
  1. % r 2 is the proportion of the phenotypic variance explained by the SNP for the association mapping population.