Table 1.
Comparison of quantitative trait nucleotide (QTN) identification for different GWAS models and genotypic datasets.
| Statistical model | Genotypic dataset | NO. of detected QTNs | NO. of common QTNs by models or datasets | NO. of non–significant QTNs | NO. of tag QTNs | R2 range (%) |
|---|---|---|---|---|---|---|
| GEMMA | ALL | 4 | 2 | 0 | 2 | 1.11–10.00 |
| FarmCPU | ALL | 25 | 6 | 0 | 6 | 1.11–12.11 |
| mrMLM | ALL | 89 | 51 | 10 | 41 | 0.66–12.72 |
| 3VmrMLM | ALL | 149 | 52 | 12 | 41 | 0.66–16.98 |
| GEMMA | GB | 1 | 1 | 0 | 1 | 1.11 |
| FarmCPU | GB | 17 | 8 | 1 | 7 | 1.11–13.30 |
| mrMLM | GB | 90 | 74 | 12 | 62 | 0.68–20.54 |
| 3VmrMLM | GB | 105 | 75 | 13 | 62 | 0.68–20.54 |
| GEMMA | RGAB | 2 | 2 | 0 | 2 | 9.34–22.42 |
| FarmCPU | RGAB | 10 | 9 | 2 | 7 | 0.54–22.42 |
| mrMLM | RGAB | 28 | 25 | 4 | 23 | 0.52–17.40 |
| 3VmrMLM | RGAB | 55 | 32 | 3 | 30 | 0.52–17.40 |
ALL, all SNPs: GB, gene SNPs: RGAB, resistance gene analog (RGA) based SNPs.