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 |