Table 3.
List of significant marker loci associated with BLUP values of grain micronutrient (Fe, Z, Cu, Mn) concentration.
| Trait | SNP ID | Chromosome | Position #(cM) | p-value | MAF | Effect∗ | -log(p-value) |
|---|---|---|---|---|---|---|---|
| Fe | AT68157 | 4D | 66.6 | 2.16E-07 | 0.20 | 3.45 | 6.67 |
| AT76904 | 2D | 89.9 | 2.35E-06 | 0.23 | 2.38 | 5.63 | |
| AT45556 | 1D | 143.5 | 4.45E-06 | 0.22 | -2.98 | 5.35 | |
| AT2276 | 7D | 51.6 | 5.80E-06 | 0.40 | 4.03 | 5.24 | |
| AT88633 | 3D | 120.8 | 2.07E-05 | 0.26 | 1.47 | 4.68 | |
| Zn | AT2707 | 2D | 19.7 | 1.08E-09 | 0.21 | 3.39 | 8.97 |
| AT65894 | 4D | 65.5 | 1.61E-05 | 0.12 | 2.80 | 4.79 | |
| AT77346 | 6D | 29.8 | 1.63E-05 | 0.18 | -2.16 | 4.79 | |
| AT92754 | 7D | 1.1 | 1.98E-05 | 0.33 | 2.59 | 4.70 | |
| Cu | AT75576 | 5D | 151.8 | 1.03E-07 | 0.28 | -0.76 | 6.99 |
| AT62347 | 1D | 55.9 | 3.86E-06 | 0.07 | 0.49 | 5.41 | |
| AT37896 | 6D | 58.6 | 2.04E-05 | 0.21 | 0.31 | 4.69 | |
| Mn | AT105092 | 6D | 144.0 | 1.55E-07 | 0.49 | -5.74 | 6.81 |
| AT102954 | 4D | 1.0 | 1.61E-07 | 0.19 | -5.96 | 6.79 | |
| AT33443 | 5D | 27.6 | 8.56E-07 | 0.23 | 2.39 | 6.07 | |
| AT359 | 5D | 89.6 | 1.60E-06 | 0.14 | 2.68 | 5.80 | |
| AT78733 | 7D | 117.5 | 2.29E-06 | 0.11 | 3.16 | 5.64 | |
| AT4038 | 7D | 71.6 | 6.51E-06 | 0.41 | 2.17 | 5.19 | |
| AT102015 | 2D | 64.6 | 1.31E-05 | 0.11 | -2.34 | 4.88 | |
MAF, minor allele frequency.
#Position of the SNPs is according to POPSEQ data (Chapman et al., 2015; Edae et al., 2015).
∗An allelic effect size is the magnitude of the effect of an allele on a phenotype. Sign of the allelic effect estimate is with respect to the nucleotide that is second in alphabetical order. For associated SNP markers, where positive effects have been reported second allele in alphabetical order is favorable, and where negative effects have been reported, the first allele is favorable. This is illustrated by allele specific boxplots in Figure 6.