Table 2.
Validation of a major spinach Fusarium wilt resistance quantitative trait locus (QTL) on chromosome 6 and the associated marker effects on reducing severity of Fusarium wilt in accessions of Spinacia turkestanica.
| SNP† | CH‡ | SNP position | lod (-log10[P]) | P-value | Marker effect§ | GWAS model# | MAF%£ |
|---|---|---|---|---|---|---|---|
| S6_38110665 | 6 | 38,110,665 | 7.91 | 1.24E-08 | Blink | 11.30% | |
| 9.24 | 5.76E-10 | -2.79 | FarmCPU | ||||
| 5.11 | 7.77E-06 | -2.63 | GLM | ||||
| 4.49 | 3.25E-05 | -2.48 | MLM | ||||
| 6.58 | 2.64E-07 | MLMM | |||||
| 5.34 | 4.54E-06 | SUPER | |||||
| 5.71 | 1.93E-06 | T.GLM | |||||
| 3.64 | 2.29E-04 | T.MLM |
†SNP = Single nucleotide polymorphism.
‡CH = Chromosome.
§SNP effect on severity of spinach Fusarium wilt. Negative values represent association with less severe Fusarium wilt.
#Genome wide association study (GWAS) models BLINK, FarmCPU, GLM, MLM, MLMM, and SUPER were run using Genome Association and Prediction Integrated Tool 3 (GAPIT 3). T.GLM (Tassel.GLM) and T.MLM (Tassel.MLM) models were run in TASSEL software.
£MAF = minor allele frequency.