Table 3. SNPs statistically associated to the seedless phenotype when analysing the panel with the MLM K + Q (K = 4) and the corresponding ranges of p- and q-values obtained.
SNPs in bold are those commonly detected when analyzing the subset. R² is the proportion of phenotypic variance explained by the markers.
| SNP ID | Chr | Position | Alleles | Location | Gene name | MAF (%) | p-values | q-values | R² | Effect | Allele |
|---|---|---|---|---|---|---|---|---|---|---|---|
| S1_2170475 | 1 | 2170475 | G/T | Exon | GSMUA_Achr1T02650 | 10.58 | - | + | 0.14 | -1.24 | K |
| -1.15 | G | ||||||||||
| S3_971104 | 3 | 971104 | A/G | UTR | GSMUA_Achr3T01360 | 50.00 | - | + | 0.16 | 0.48 | A |
| 0.01 | R | ||||||||||
| S3_22358632 | 3 | 22358632 | A/T | Intergenic | 38.46 | - | + | 0.16 | 0.41 | A | |
| 0.08 | W | ||||||||||
| S3_23751148 | 3 | 23751148 | A/G | Intron | GSMUA_Achr3P22900 | 10.48 | *** | ++ | 0.25 | -0.74 | A |
| -0.20 | R | ||||||||||
| S4_5366421 | 4 | 5366421 | T/C | Exon | GSMUA_Achr4T07200 | 28.10 | - | + | 0.14 | 0.42 | C |
| 0.06 | Y | ||||||||||
| S5_11617038 | 5 | 11617038 | G/- | Intron | GSMUA_Achr5T15610 | 18.57 | - | + | 0.17 | 0.42 | C |
| -0.12 | G | ||||||||||
| S7_21735706 | 7 | 21735706 | G/T | Intron | GSMUA_Achr7T18900 | 48.57 | - | + | 0.15 | 0.50 | G |
| 0.17 | K | ||||||||||
| S7_21735724 | 7 | 21735724 | -/T | Intron | GSMUA_Achr7T18900 | 34.29 | - | + | 0.17 | 0.45 | T |
| 0.17 | A | ||||||||||
| S7_21735725 | 7 | 21735725 | T/- | Intron | GSMUA_Achr7G18900 | 17.14 | - | ++ | 0.18 | 0.49 | A |
| -0.08 | T | ||||||||||
| S7_21735729 | 7 | 21735729 | T/C | Intron | GSMUA_Achr7G18900 | 18.57 | ** | ++ | 0.19 | 0.47 | C |
| -0.10 | T | ||||||||||
| S7_21735767 | 7 | 21735767 | G/A | Intron | GSMUA_Achr7G18900 | 18.09 | ** | ++ | 0.19 | 0.48 | A |
| -0.07 | G | ||||||||||
| S7_21742629 | 7 | 21742629 | C/T | Intergenic | 26.44 | - | + | 0.14 | 0.40 | T | |
| -0.07 | G | ||||||||||
| S7_21742664 | 7 | 21742664 | T/G | Intergenic | 39.90 | - | + | 0.15 | 0.51 | T | |
| 0.12 | K | ||||||||||
| S7_21742673 | 7 | 21742673 | C/G | Intergenic | 39.90 | - | + | 0.15 | 0.51 | C | |
| 0.12 | K | ||||||||||
| S7_21920043 | 7 | 21920043 | G/A | Intron | GSMUA_Achr7T19120 | 42.86 | - | + | 0.16 | 0.45 | G |
| -0.02 | C | ||||||||||
| S9_3878154 | 9 | 3878154 | G/A | Exon | GSMUA_Achr9G06060 | 11.43 | - | + | 0.15 | -0.39 | G |
| -0.16 | W | ||||||||||
| S9_30886263 | 9 | 30886263 | G/A | Exon | GSMUA_Achr9T26460 | 44.76 | - | + | 0.14 | 0.39 | G |
| 0.03 | R | ||||||||||
| S10_5800489 | 10 | 5800489 | C/T | intergenic | 10.19 | *** | ++ | 0.36 | -0.94 | Y | |
| -0.08 | C | ||||||||||
| S10_9284262 | 10 | 9284262 | C/T | Intergenic | 40.59 | *** | ++ | 0.30 | 0.80 | T | |
| -0.01 | Y | ||||||||||
| S11_15250304 | 11 | 15250304 | T/- | Intron | GSMUA_Achr11T14210 | 42.38 | ** | ++ | 0.20 | -0.70 | T |
| -0.05 | W | ||||||||||
| S11_24122623 | 11 | 24122623 | A/G | intergenic | 27.14 | - | + | 0.14 | -0.68 | A | |
| -0.59 | R | ||||||||||
| Total number of significant SNPs | 15 | 21 |
¶: Major/Minor
-: Not applicable
For 3912 markers with MAF>10%, the Bonferroni-corrected thresholds for the p-values were 2.6e-6 (α = 0.01) coded as *** and 1.3e-5 (α = 0.05) coded as ** FDR results (q-values) were coded as ++ (α = 0.01) and + (α = 0.05).