Table 1.
List of SNP markers significantly associated with P. effusa race 5 resistance in spinach population segregating for RPF3 resistance from Whale.
| SNP | Chr | Position | Alleles (Ref/ Alt) | MAF | LOD (-log10 P) value | R2 | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| TASSEL | GENESIS | GAPIT | Mean LOD value | |||||||||||||||
| SMR | GLM | MLM | LMM | GLM.R | MLM.R | MLMM | SUPER | FarmCPU | BLINK | SMR | GLM.R | GENESIS | ||||||
| GWAS analysis using SNP markers called upon Monoe-Viroflay assembly | ||||||||||||||||||
| Chr3_1253998 | 3 | 1253998 | G/T | 0.45 | 26.39 | 23.93 | 12.73 | 12.08 | 13.96 | 11.18 | 15.17 | 24.52 | 9.99 | 12.82 | 16.28 | 56.75 | 35.31 | 39.98 |
| Chr3_1254008 | 3 | 1254008 | G/T | 0.45 | 26.14 | 23.12 | 12.72 | 11.81 | 13.76 | 11.03 | 0.01 | 24.52 | 0.41 | 0.20 | 12.37 | 56.65 | 34.69 | 39.00 |
| Chr3_2735424 | 3 | 2735424 | T/A | 0.26 | 15.96 | 15.83 | 5.47 | 6.82 | 10.52 | 4.99 | 1.40 | 19.56 | 1.30 | 0.62 | 8.25 | 38.95 | 25.01 | 21.53 |
| Chr3_2736368 | 3 | 2736368 | C/T | 0.27 | 13.84 | 13.40 | 5.11 | 6.02 | 9.78 | 4.01 | 0.87 | 18.61 | 0.45 | 0.31 | 7.24 | 34.07 | 22.92 | 18.74 |
| Chr3_2736465 | 3 | 2736465 | T/C | 0.26 | 16.89 | 16.03 | 6.49 | 7.82 | 10.97 | 5.59 | 1.61 | 19.86 | 1.22 | 0.85 | 8.73 | 38.13 | 26.32 | 25.01 |
| Chr3_2736973 | 3 | 2736973 | G/A | 0.24 | 15.49 | 15.85 | 6.24 | 7.79 | 10.43 | 4.90 | 0.86 | 19.36 | 0.63 | 0.23 | 8.18 | 35.62 | 24.76 | 24.90 |
| Chr3_2736989 | 3 | 2736989 | T/C | 0.25 | 14.62 | 15.27 | 5.83 | 7.57 | 10.28 | 4.63 | 0.90 | 19.32 | 0.24 | 0.31 | 7.90 | 33.84 | 24.34 | 24.13 |
| Chr3_2737221 | 3 | 2737221 | A/G | 0.24 | 12.86 | 13.49 | 5.68 | 6.75 | 10.17 | 5.45 | 1.21 | 18.57 | 0.43 | 0.32 | 7.49 | 30.00 | 24.02 | 21.26 |
| Chr3_2737270 | 3 | 2737270 | G/A | 0.32 | 19.40 | 20.37 | 7.84 | 8.99 | 11.71 | 6.70 | 2.69 | 14.80 | 0.98 | 0.98 | 9.45 | 46.70 | 28.46 | 29.08 |
| Chr3_2737288 | 3 | 2737288 | T/C | 0.23 | 16.94 | 17.04 | 7.32 | 8.35 | 11.72 | 6.95 | 2.30 | 20.18 | 1.34 | 0.97 | 9.31 | 37.68 | 28.52 | 26.86 |
| Chr3_2738051 | 3 | 2738051 | T/G | 0.30 | 17.91 | 17.95 | 7.05 | 8.20 | 11.63 | 6.48 | 2.26 | 14.79 | 1.79 | 0.59 | 8.86 | 41.47 | 28.23 | 26.31 |
| Chr3_2738114 | 3 | 2738114 | G/A | 0.24 | 16.58 | 16.72 | 6.54 | 7.97 | 12.12 | 6.90 | 2.21 | 22.43 | 1.02 | 0.80 | 9.33 | 36.52 | 29.68 | 25.52 |
| Chr3_2738382 | 3 | 2738382 | A/G | 0.29 | 20.45 | 20.83 | 8.30 | 9.58 | 12.90 | 7.22 | 3.05 | 22.33 | 11.99 | 4.56 | 12.12 | 45.54 | 32.04 | 31.16 |
| Chr3_2739015 | 3 | 2739015 | G/A | 0.24 | 17.77 | 17.23 | 6.49 | 7.45 | 12.14 | 6.40 | 1.91 | 21.49 | 2.87 | 0.59 | 9.43 | 40.61 | 29.75 | 23.73 |
| Chr3_2741024 | 3 | 2741024 | A/G | 0.26 | 19.40 | 18.43 | 7.92 | 8.54 | 10.72 | 5.51 | 0.47 | 19.31 | 1.54 | 0.08 | 9.19 | 44.66 | 25.58 | 27.53 |
| Chr3_2741123 | 3 | 2741123 | C/G | 0.23 | 16.18 | 16.65 | 7.20 | 8.40 | 11.91 | 6.87 | 0.73 | 15.92 | 3.72 | 4.66 | 9.22 | 35.16 | 29.08 | 27.01 |
| Chr3_2741149 | 3 | 2741149 | C/T | 0.22 | 16.77 | 17.09 | 7.24 | 8.15 | 12.30 | 6.89 | 0.96 | 16.12 | 4.22 | 0.81 | 9.06 | 36.52 | 30.22 | 26.14 |
| Chr3_2741203 | 3 | 2741203 | A/G | 0.22 | 16.32 | 16.82 | 6.73 | 8.14 | 11.82 | 6.40 | 0.50 | 15.30 | 3.49 | 0.98 | 8.65 | 36.06 | 28.79 | 26.12 |
| Chr3_2741229 | 3 | 2741229 | G/A | 0.22 | 16.46 | 16.65 | 7.10 | 8.22 | 11.71 | 6.45 | 0.06 | 15.07 | 3.50 | 0.77 | 8.60 | 36.31 | 28.48 | 26.41 |
| Chr3_2741241 | 3 | 2741241 | G/T | 0.22 | 17.17 | 17.41 | 7.31 | 8.10 | 11.89 | 6.75 | 13.76 | 21.08 | 3.47 | 1.06 | 10.80 | 38.26 | 29.00 | 25.98 |
| GWAS analysis using SNP markers called upon Sp75 assembly | ||||||||||||||||||
| Chr3_1192667 | 3 | 1192667 | A/T | 0.38 | 27.18 | 25.24 | 16.13 | 10.60 | 14.45 | 8.86 | 4.91 | 1.94 | 1.70 | 1.34 | 11.23 | 0.59 | 35.67 | 0.42 |
| Chr3_1192826 | 3 | 1192826 | C/G | 0.41 | 26.12 | 24.85 | 24.41 | 10.87 | 14.78 | 8.91 | 0.29 | 1.52 | 2.05 | 0.41 | 11.42 | 0.54 | 36.69 | 0.43 |
| Chr3_1193578 | 3 | 1193578 | T/C | 0.41 | 21.38 | 20.08 | 10.12 | 10.07 | 13.83 | 8.25 | 0.31 | 0.91 | 1.88 | 0.17 | 8.70 | 0.46 | 33.79 | 0.40 |
| Chr3_1194293 | 3 | 1194293 | C/T | 0.37 | 30.92 | 28.62 | 27.86 | 11.21 | 15.84 | 10.50 | 0.65 | 2.05 | 2.29 | 0.77 | 13.07 | 0.61 | 39.99 | 0.45 |
| Chr3_1194847 | 3 | 1194847 | T/G | 0.40 | 31.21 | 28.78 | 18.05 | 12.26 | 16.37 | 11.14 | 1.88 | 1.32 | 2.67 | 5.36 | 12.90 | 0.60 | 41.71 | 0.49 |
| Chr3_1195703 | 3 | 1195703 | C/T | 0.44 | 26.45 | 24.36 | 14.33 | 11.28 | 15.22 | 9.43 | 1.46 | 1.61 | 2.09 | 0.14 | 10.64 | 0.57 | 38.06 | 0.45 |
| Chr3_1222338 | 3 | 1222338 | A/C | 0.46 | 16.37 | 16.72 | 7.59 | 10.09 | 12.93 | 6.74 | 1.13 | 0.61 | 0.64 | 0.12 | 7.29 | 0.36 | 31.10 | 0.40 |
| Chr3_1222475 | 3 | 1222475 | C/G | 0.49 | 20.47 | 21.21 | 11.88 | 11.73 | 14.25 | 8.46 | 1.02 | 1.19 | 1.11 | 0.19 | 9.15 | 0.43 | 35.05 | 0.47 |
| Chr3_1222554 | 3 | 1222554 | C/A | 0.49 | 23.66 | 25.04 | 13.90 | 12.89 | 15.54 | 9.70 | 2.60 | 2.18 | 2.10 | 3.56 | 11.12 | 0.49 | 39.04 | 0.52 |
| GWAS analysis using SNP markers called upon Sp75 assembly | ||||||||||||||||||
| Chr3_1222956 | 3 | 1222956 | A/G | 0.48 | 21.62 | 22.28 | 11.44 | 12.31 | 15.26 | 9.42 | 1.33 | 0.49 | 0.84 | 0.18 | 9.52 | 0.48 | 38.16 | 0.50 |
| Chr3_1223036 | 3 | 1223036 | C/T | 0.49 | 23.65 | 24.52 | 14.25 | 12.68 | 15.38 | 9.83 | 1.75 | 0.76 | 0.74 | 0.08 | 10.36 | 0.50 | 38.54 | 0.51 |
| Chr3_1223119 | 3 | 1223119 | G/A | 0.49 | 25.97 | 26.42 | 15.61 | 13.15 | 15.86 | 10.95 | 2.27 | 0.98 | 0.29 | 0.51 | 11.20 | 0.53 | 40.07 | 0.53 |
| Chr3_1223518 | 3 | 1223518 | A/T | 0.49 | 23.40 | 23.75 | 14.12 | 13.22 | 16.28 | 10.90 | 2.11 | 0.61 | 0.13 | 1.10 | 10.56 | 0.51 | 41.41 | 0.54 |
| Chr3_1223573 | 3 | 1223573 | A/T | 0.49 | 22.42 | 22.20 | 12.31 | 12.67 | 15.81 | 10.18 | 1.69 | 0.47 | 0.16 | 1.06 | 9.90 | 0.49 | 39.90 | 0.51 |
| Chr3_1239348 | 3 | 1239348 | T/C | 0.49 | 30.83 | 28.59 | 23.74 | 14.12 | 17.36 | 12.08 | 7.84 | 1.08 | 20.51 | 5.67 | 16.18 | 0.63 | 44.92 | 0.57 |
| Chr3_1754331 | 3 | 1754331 | G/T | 0.49 | 24.45 | 22.63 | 12.02 | 10.81 | 13.14 | 7.37 | 1.32 | 0.00 | 0.10 | 0.24 | 9.21 | 0.53 | 31.71 | 0.43 |
| Chr3_1762159 | 3 | 1762159 | T/C | 0.44 | 30.90 | 30.24 | 19.66 | 12.16 | 15.08 | 9.74 | 5.97 | 0.49 | 6.79 | 5.54 | 13.66 | 0.61 | 37.61 | 0.49 |
SNP name defined as SNP position on the chromosome.
MAF is monor allele frequecy.
LOD (-LOG10P) value, with P value from the SMR, GLM, MLM models in TASSEL; logistic mixed model (LMM) in GENESIS; and GLM, MLM, MLMM, SUPER, FarmCPU, and BLINK models in GAPIT 3 R package.
Percentage of phenotypic variation (R2) explained by SNPs generated by TASSEL SMR model, GAPIT GLM model, and by GENESIS program.