Table 3.
Summary of associations identified by Multi-Locus Mixed Model (MLMM) at the optimal models according to the EBIC criterion for flowering and ripening periods in the whole population and in the six individual collections.
| Population | SNP code | SNP short name | No. Cofactora | Location of the SNPs | Alleles | p-value | MAF | |
|---|---|---|---|---|---|---|---|---|
| Chromosome | Position | |||||||
| FLOWERING PERIOD | ||||||||
| Whole population | FB_AFFY_0496090 | SNP.9-1 | 1 | 9 | 530,386 | G/Tb | 1.33E-08 | 0.11 |
| Whole population | FB_AFFY_0495650 | SNP.9-2 | 2 | 9 | 557,419 | A/G | 6.81E-08 | 0.13 |
| INRA | FB_AFFY_0495650 | SNP.9-2 | 1 | 9 | 557,419 | A/G | 1.06E-12 | 0.18 |
| RBIPH | FB_AFFY_6830175 | SNP.4-1 | 1 | 4 | 968,334 | C/T | 3.16E-09 | 0.01 |
| RBIPH | FB_AFFY_1629518 | SNP.9-3 | 2 | 9 | 925,476 | A/G | 8.01E-08 | 0.14 |
| NFC | FB_AFFY_6873601 | SNP.4-2 | 4 | 4 | 7,719,622 | A/G | 3.94E-07 | 0.24 |
| NFC | FB_AFFY_7355751 | SNP.9-4 | 2 | 9 | 1,938,744 | C/T | 3.15E-08 | 0.11 |
| NFC | FB_AFFY_2782466 | SNP.11-1 | 1 | 11 | 12,422,656 | A/C | 8.30E-09 | 0.02 |
| NFC | FB_AFFY_9818101 | SNP.12-1 | 3 | 12 | 14,536,815 | C/T | 5.35E-08 | 0.15 |
| RIPENING PERIOD | ||||||||
| Whole population | FB_AFFY_6730867 | SNP.3-3 | 4 | 3 | 30,430,113 | A/Gc | 6.76E-15 | 0.10 |
| Whole population | FB_AFFY_7541229 | SNP.3-4 | 5 | 3 | 30,465,002 | C/T | 8.51E-10 | 0.09 |
| Whole population | FB_AFFY_4981462 | SNP.3-6 | 2 | 3 | 30,700,183 | C/T | 4.39E-19 | 0.18 |
| Whole population | FB_AFFY_1209620 | SNP.3-7 | 1 | 3 | 30,726,252 | A/G | 1.28E-13 | 0.41 |
| Whole population | FB_AFFY_3795860 | SNP.10-1 | 6 | 10 | 38,390,484 | A/G | 1.76E-08 | 0.23 |
| Whole population | FB_AFFY_6370928 | SNP.16-1 | 3 | 16 | 9,146,297 | C/T | 5.16E-12 | 0.14 |
| INRA | FB_AFFY_1253936 | SNP.3-5 | 1 | 3 | 30,590,166 | A/C | 3.03E-14 | 0.08 |
| UNIBO | FB_AFFY_1253936 | SNP.3-5 | 1 | 3 | 30,590,166 | A/C | 6.75E-09 | 0.06 |
| CRA-W | FB_AFFY_4741632 | SNP.3-2 | 1 | 3 | 30,318,639 | A/G | 6.71E-08 | 0.11 |
| RBIPH | FB_AFFY_4981462 | SNP.3-6 | 1 | 3 | 30,700,183 | C/T | 3.60E-10 | 0.20 |
| RBIPH | FB_AFFY_4836781 | SNP.15-1 | 2 | 15 | 10,377,731 | C/T | 3.18E-08 | 0.37 |
| NFC | FB_AFFY_4981462 | SNP.3-6 | 1 | 3 | 30,700,183 | C/T | 1.37E-18 | 0.14 |
| SLU | FB_AFFY_0899559 | SNP.3-1 | 4 | 3 | 24,220,838 | A/G | 7.21E-07 | 0.10 |
| SLU | FB_AFFY_1209620 | SNP.3-7 | 1 | 3 | 30,726,252 | A/G | 7.51E-15 | 0.33d |
| SLU | FB_AFFY_6239519 | SNP.13-1 | 3 | 13 | 1,889,560 | G/T | 1.41E-07 | 0.24 |
| SLU | FB_AFFY_3879540 | SNP.16-2 | 2 | 16 | 10,298,660 | G/T | 2.34E-07 | 0.27 |
Order of inclusion of the SNPs at the optimal model in MLMM according to the EBIC criterion.
The allele associated with an early flowering period is highlighted in bold. The alternative allele is thus associated with a late flowering period.
The allele associated with an early ripening period is highlighted in bold. The alternative allele is thus associated with a late ripening period.
The allele found in SLU with the lowest frequency was the opposite to the one that appeared in the lowest frequency in the whole population and the other five individual collections.