Table 2.
SNP markers significantly associated with the late blight and potato cyst nematode resistance phenotype in different years using complete and reduced marker data set.
| Trait | Model | Marker | Chr | Position | Ref allele | Alt allele | Threshold | Score | Effect | R2 | P value |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Full marker set | |||||||||||
| AUDPC18 | additive | chr11_5176739 | Chr11 | 5176739 | T | G | 6.12 | 8.19 | -365.24 | 0.156 | 0 |
| AUDPC18 | 1-dom-alt | chr08_1111466 | Chr08 | 1111466 | T | G | 6.1 | 6.21 | 454.94 | 0.123 | 0 |
| AUDPC18 | 1-dom-alt | chr11_5176739 | Chr11 | 5176739 | T | G | 6.12 | 8.19 | -365.24 | 0.156 | 0 |
| AUDPC19 | 1-dom-alt | chr11_45392300 | chr11 | 45392300 | A | T | 6.1 | 6.33 | -741.63 | 0.171 | 0 |
| GP20 | additive | chr03_30051088 | chr03 | 30051088 | A | G | 6.12 | 7.35 | 0.69 | 0.157 | 0 |
| GP21 | 1-dom-alt | chr01_79870255 | chr01 | 79870255 | C | T | 6.1 | 6.38 | -1.72 | 0.078 | 0 |
| GP21 | 1-dom-ref | chr05_39730271 | chr05 | 39730271 | C | T | 6.1 | 6.37 | -2.65 | 0.04 | 0.012 |
| GP21 | 1-dom-ref | chr10_29357976 | chr10 | 29357976 | C | T | 6.1 | 7.6 | -1.95 | 0.058 | 0.003 |
| GR20 | 1-dom-alt | chr01_48615182 | chr01 | 48615182 | C | T | 6.11 | 6.69 | -1.51 | 0.066 | 0 |
| GR20 | additive | chr03_27049362 | chr03 | 27049362 | A | G | 6.12 | 7 | 0.91 | 0.115 | 0 |
| GR20 | 1-dom-ref | chr05_52055419 | chr05 | 52055419 | A | G | 6.11 | 6.21 | 1.30 | 0.045 | 0.003 |
| GR20 | additive | chr12_53396900 | chr12 | 53396900 | A | G | 6.12 | 6.86 | -0.80 | 0.048 | 0.003 |
| GR20 | additive | chr12_619482 | Chr12 | 619482 | A | G | 5.55 | 6.41 | -0.42 | 0.083 | 0 |
| GR21 | 1-dom-alt | chr04_43994066 | chr04 | 43994066 | A | G | 6.1 | 6.26 | 1.72 | 0.095 | 0 |
| GR21 | 1-dom-alt | chr10_11705153 | chr10 | 11705153 | C | T | 6.1 | 6.23 | 2.59 | 0.217 | 0 |
| Reduced marker set | |||||||||||
| AUDPC18 | additive | chr03_2054715 | Chr03 | 2054715 | G | T | 5.55 | 5.58 | -298.04 | 0.105 | 0 |
| AUDPC19 | additive | chr04_5755401 | Chr04 | 5755401 | C | T | 5.54 | 5.55 | -125.50 | 0.127 | 0 |
| AUDPC19 | 1-dom-ref | chr05_13326227 | Chr05 | 13326227 | A | G | 5.53 | 6.06 | -263.30 | 0.099 | 0 |
| AUDPC20 | additive | chr11_44083171 | Chr11 | 44083171 | A | G | 5.55 | 5.6 | 50.96 | 0.107 | 0 |
| GP20 | additive | chr01_62889722 | Chr01 | 62889722 | C | T | 5.55 | 5.83 | -0.40 | 0.128 | 0 |
| GP20 | 1-dom-ref | chr10_29996650 | Chr10 | 29996650 | A | G | 5.54 | 5.73 | -1.52 | 0.121 | 0 |
| GP21 | 1-dom-alt | chr10_45333027 | Chr10 | 45333027 | A | G | 5.53 | 7.44 | 2.84 | 0.024 | 0.053 |
| GP21 | 1-dom-ref | chr10_29358030 | Chr10 | 29358030 | A | G | 5.53 | 6.33 | -1.88 | 0.065 | 0.001 |
| GP21 | 1-dom-alt | chr11_43021827 | Chr11 | 43021827 | C | T | 5.53 | 5.84 | -1.27 | 0.065 | 0.001 |
| GR20 | 1-dom-alt | chr01_14013398 | Chr01 | 14013398 | A | G | 5.54 | 5.6 | -1.42 | 0.109 | 0 |
| GR20 | additive | chr02_43988105 | Chr02 | 43988105 | A | T | 5.55 | 5.69 | 0.69 | 0.115 | 0 |
| GR20 | 1-dom-alt | chr05_47262811 | Chr05 | 47262811 | C | T | 5.54 | 5.83 | -1.66 | 0.065 | 0 |
| GR20 | additive | chr12_619482 | Chr12 | 619482 | A | G | 5.55 | 6.41 | -0.42 | 0.083 | 0 |
| GR21 | additive | chr10_29388315 | Chr10 | 29388315 | A | G | 5.55 | 5.64 | -0.66 | 0.088 | 0 |
| GR21 | 1-dom-alt | chr03_23982469 | Chr03 | 23982469 | A | G | 5.53 | 6.81 | -2.07 | 0.129 | 0 |
Chr, Chromosome; Ref,Reference; Alt-Alternate; 1-dom-alt, dominant alternate; 1-dom-ref, dominant reference; AUDPC18, Late Blight 2018; AUDPC19, Late Blight 2019; AUDPC20, Late Blight 2020; GP20, Globodera pallida 2020; GP21, Globodera pallida 21; GR20, Globodera rostochiensis 20; GR21, Globodera rostochiensis 21.