Table 4.
Single nucleotide polymorphism (SNP) markers associated with resistance P3.4.0, S10.2 and K5.1 isolates, revealed by GLM + PCA + Q analysis according p-value
| Isolate | p-value | Marker | chr | Position | cM | Allele | Minor Allele | SNP associated with resistance |
|---|---|---|---|---|---|---|---|---|
| P3.4.0 | 7.64E-07 | SCRI_RS_239642a | 6H | 357492232 | 55.4 | A/G | A(0.22) | A(0.83) |
| P3.4.0 | 6.72E-07 | SCRI_RS_224389a | 6H | 360336381 | 55.4 | C/T | C(0.22) | C(0.83) |
| P3.4.0 | 2.30E-07 | JHI-Hv50k-2016-104859a | 2H | 639342580 | 71-74.1 | A/G | G(0.18) | A(0.50) |
| P3.4.0 | 1.58E-06 | BOPA2_12_31445a | 2H | 639288665 | 71-74.1 | A/G | G(0.20) | A(0.50) |
| P3.4.0 | 9.13E-06 | JHI-Hv50k-2016-35839b | 1H | 463250609 | 62.3-62.8 | T/G | T(0.38) | G(0.75) |
| P3.4.0 | 1.60E-05 | JHI-Hv50k-2016-398663b | 6H | 359349968 | 55.4 | T/C | C(0.25) | C(0.83) |
| P3.4.0 | 1.60E-05 | SCRI_RS_138529b | 6H | 86866524 | 55.4 | T/C | C(0.25) | C(0.83) |
| P3.4.0 | 2.59E-05 | JHI-Hv50k-2016-104508b | 2H | 638564394 | 71–74.1 | C/T | T(0.24) | T(0.50) |
| P3.4.0 | 2.59E-05 | JHI-Hv50k-2016-104565b | 2H | 638636071 | C/T | T(0.24) | T(0.50) | |
| P3.4.0 | 2.59E-05 | JHI-Hv50k-2016-104567b | 2H | 638636277 | C/T | T(0.24) | T(0.50) | |
| P3.4.0 | 2.59E-05 | JHI-Hv50k-2016-104667b | 2H | 638690222 | G/T | T(0.24) | T(0.50) | |
| P3.4.0 | 2.82E-05 | JHI-Hv50k-2016-104669b | 2H | 638690416 | A/C | C(0.24) | A(0.50) | |
| P3.4.0 | 4.35E-05 | JHI-Hv50k-2016-33086b | 1H | 438893078 | 57.3-58.2 | C/A | A(0.26) | C(0.75) |
| P3.4.0 | 4.64E-05 | JHI-Hv50k-2016-156591b | 3H | 17271039 | 12.1–17.4 | T/C | C(0.23) | T(0.75) |
| P3.4.0 | 4.77E-05 | JHI-Hv50k-2016-156539b | 3H | 16631590 | G/T | T(0.14) | G(0.75) | |
| P3.4.0 | 4.77E-05 | JHI-Hv50k-2016-156576b | 3H | 17177586 | T/C | C(0.14) | T(0.75) | |
| P3.4.0 | 4.77E-05 | JHI-Hv50k-2016-156584b | 3H | 17269072 | C/G | C(0.14) | G(0.75) | |
| P3.4.0 | 5.54E-05 | JHI-Hv50k-2016-33097b | 1H | 439174674 | 57.3–58.2 | G/A | A(0.27) | G(0.75) |
| P3.4.0 | 5.54E-05 | JHI-Hv50k-2016-33109b | 1H | 439297538 | G/A | A(0.27) | C(0.75) | |
| P3.4.0 | 6.58E-05 | JHI-Hv50k-2016-156594b | 3H | 17292680 | 12.1–17.4 | A/T | T(0.22) | A(0.75) |
| P3.4.0 | 6.66E-05 | JHI-Hv50k-2016-156586b | 3H | 17270441 | T/A | T(0.23) | A(0.75) | |
| P3.4.0 | 7.32E-05 | JHI-Hv50k-2016-33099b | 1H | 439176975 | 57.3–58.2 | C/T | T(0.26) | C(0.75) |
| P3.4.0 | 7.32E-05 | JHI-Hv50k-2016-33104b | 1H | 439177729 | T/C | C(0.26) | T(0.75) | |
| P3.4.0 | 7.59E-05 | JHI-Hv50k-2016-398720b | 6H | 359701468 | 55.4 | C/T | T(0.10) | C(0.58) |
| P3.4.0 | 7.59E-05 | JHI-Hv50k-2016-398886b | 6H | 361528770 | C/T | C(0.10) | T(0.58) | |
| P3.4.0 | 7.59E-05 | JHI-Hv50k-2016-398894b | 6H | 361531190 | C/T | C(0.10) | T(0.58) | |
| P3.4.0 | 9.74E-05 | JHI-Hv50k-2016-33120b | 1H | 439541073 | 57.3-58.2 | C/G | G(0.27) | C(0.75) |
| P3.4.0 | 1.01E-04 | JHI-Hv50k-2016-36398b | 1H | 467931082 | 62.3-62.8 | T/G | G(0.27) | T(0.83) |
| S10.2 | 1.10E-05 | JHI-Hv50k-2016-392723c | 6H | 155949390 | 52.6–53.8 | A/G | G(0.48) | A(0.86) |
| S10.2 | 1.10E-05 | JHI-Hv50k-2016-393052c | 6H | 163763506 | T/A | T(0.48) | A(0.86) | |
| S10.2 | 2.98E-05 | JHI-Hv50k-2016-392656c | 6H | 153234073 | A/G | A(0.47) | T(0.86) | |
| S10.2 | 7.02E-05 | JHI-Hv50k-2016-391875c | 6H | 142513704 | A/C | A(0.30) | C(1) | |
| S10.2 | 7.02E-05 | BOPA2_12_30021c | 6H | 156957594 | A/G | A(0.30) | G(1) | |
| K5.1 | 1.41E-04 | JHI-Hv50k-2016-215624c | 3H | 668951958 | 135.6-137.5 | A/C | C(0.11) | A(1) |
| K5.1 | 1.45E-04 | JHI-Hv50k-2016-33160c | 1H | 441912080 | 57.3-58.2 | G/A | A(0.21) | A(0.55) |
aSignificant SNPs according the Bonferroni correction
bSignificant SNPs according the FDR
cSuggestive SNPs