Table 2.
List of SNPs significantly associated with APR to the Ug99 race group in Kenya and Ethiopia. ‘Chromosome 0’ includes all unmapped SNP markers
| SNPa | Chrb | Pos (cM) | P value | R2 (%)c | KenOff13d | KenMain13e | EthOff13f | EthOff14g |
|---|---|---|---|---|---|---|---|---|
| IWB1351 | 0 | 0.0 | 9.18E-04 | 1.4 | - | - | - | + |
| IWB11987 | 2.71E-04 | 4.0 | - | - | - | - | ||
| IWB13304 | 9.18E-04 | 1.4 | - | - | - | + | ||
| IWB20617 | 8.92E-04 | 0.5 | - | - | - | - | ||
| IWB40153 | 9.18E-04 | 1.4 | - | - | - | + | ||
| IWB65634 | 2.18E-04 | 3.9 | - | - | - | - | ||
| IWA3120 | 1B | 90.3 | 9.07E-04 | 0.6 | - | - | - | - |
| IWB21176 | 9.64E-04 | 0.6 | - | - | + | - | ||
| IWB31027 | 9.64E-04 | 0.6 | - | - | + | - | ||
| IWB56771 | 9.34E-04 | 0.6 | - | - | + | - | ||
| IWB59663 | 9.64E-04 | 0.6 | - | - | + | - | ||
| IWB49915 | 2A | 122.5 | 9.18E-04 | 1.4 | - | - | - | + |
| IWB49914 | 123.6 | 9.18E-04 | 1.4 | - | - | - | + | |
| IWB22672 | 159.7 | 9.98E-04 | 0.6 | - | - | + | - | |
| IWB2369 | 2B | 48.5 | 7.68E-04 | 0.4 | - | - | - | - |
| IWA4275 | 105.9 | 8.75E-04 | 1.4 | - | - | - | - | |
| IWA8534 | 126.1 | 1.80E-04 | 0.3 | - | + | - | - | |
| IWB23660 | 126.3 | 1.79E-04 | 0.3 | - | + | - | - | |
| IWB25868 | 3.11E-04 | 0.7 | - | + | - | - | ||
| IWB69631 | 3.11E-04 | 0.7 | - | + | - | - | ||
| IWB25869 | 126.5 | 3.11E-04 | 0.7 | - | + | - | - | |
| IWB32143 | 157.2 | 5.05E-04 | 4.6 | - | - | - | - | |
| SNPa | Chrb | Pos (cM) | P value | R2 (%)c | KenOff13d | KenMain13e | EthOff13f | EthOff14g |
| IWB8481 | 2D | 9.2 | 8.44E-04 | 0.5 | - | - | - | - |
| IWA5203 | 3B | 11.5 | 7.97E-04 | 0.4 | - | - | - | - |
| IWB30730 | 7.74E-04 | 1.3 | - | - | - | - | ||
| IWB12193 | 11.6 | 3.24E-04 | 4.2 | - | + | - | - | |
| IWB49924 | 5.65E-04 | 0.2 | - | - | - | - | ||
| IWB65737 | 9.15E-04 | 0.6 | - | - | - | - | ||
| IWB60424 | 13.8 | 5.02E-04 | 0.1 | - | - | - | - | |
| IWB36021 | 14.1 | 8.31E-04 | 1.3 | - | - | - | - | |
| IWA2493 | 32.2 | 1.49E-04 | 0.2 | - | - | + | - | |
| IWB40004 | 4A | 30.9 | 9.12E-04 | 0.6 | - | + | - | - |
| IWB52694 | 43.4 | 9.96E-05 | 3.2 | - | + | - | - | |
| IWB46973 | 47.0 | 8.26E-04 | 1.3 | - | + | - | - | |
| IWB56556 | 7.54E-04 | 1.3 | - | - | - | - | ||
| IWB67877 | 8.34E-04 | 1.3 | - | - | - | - | ||
| IWB47184 | 5A | 69.6 | 3.44E-04 | 0.3 | - | - | + | - |
| IWA233 | 6A | 66.0 | 8.48E-04 | 1.3 | - | + | - | - |
| IWB24757 | 6B | 119.7 | 6.33E-04 | 1.1 | - | - | - | - |
| IWB35697 | 1.77E-05 | 1.3 | - | - | + | + | ||
| IWB6474 | 6.33E-04 | 1.1 | - | - | - | - | ||
| IWB45581 | 120.6 | 3.00E-04 | 0.6 | - | - | - | - | |
| IWB5070 | 7A | 211.0 | 2.19E-04 | 3.9 | - | - | - | - |
| IWB1874 | 212.7 | 3.18E-04 | 0.3 | - | - | - | - | |
| IWB4830 | 4.50E-04 | 4.5 | - | - | + | - | ||
| IWB62560 | 213.2 | 2.30E-04 | 0.6 | - | - | - | - | |
| IWB47548 | 7B | 153.4 | 6.50E-04 | 0.3 | - | - | - | - |
| IWA4175 | 177.1 | 9.52E-04 | 0.6 | - | - | - | - |
aUnderlined SNP markers were detected during the ‘combined’ mapping approach but not during the ‘APR-specific’ mapping approach. SNP markers in bold were detected in both mapping approaches
bChr ‘0’ indicates unmapped SNPs that were significant in the analysis
cR2Indicates percent of phenotypic variation explained by the significant locus
d-gThe ‘+’ sign indicates that the SNP was also detected in GWAS results in each of the environments. The ‘-‘ sign indicates that the SNP was detected only in combined analysis of all environments, and not in individual environments