Table 4.
(A) Pairwise LD between the two SNPs associated with flowering period in the whole population (A1) and in the three geographic groups: North+East (A2), West (A3), and South (A4). (B) Pairwise LD between the four SNPs associated with ripening period on chromosome 3 in the whole population (B1) and the three geographic groups: North+East (B2), West (B3), and South (B4).
| A | B | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| (A1) Whole population | (B1) Whole population | ||||||||
| SNPs as cofactors | SNP.9-1 | SNP.9-2 | MAF | SNPs as cofactors | SNP.3-3 | SNP.3-4 | SNP.3-6 | SNP.3-7 | MAF |
| SNP.9-1 | 1.00 | 0.12 | 0.11 | SNP.3-3 | 1.00 | 0.55 | 0.31 | 0.02 | 0.10 |
| SNP.9-2 | 0.27 | 1.00 | 0.13 | SNP.3-4 | 0.71 | 1.00 | 0.27 | 0.06 | 0.09 |
| SNP.3-6 | 0.56 | 0.54 | 1.00 | 0.22 | 0.18 | ||||
| (A2) North+East group | SNP.3-7 | 0.11 | 0.06 | 0.22 | 1.00 | 0.41 | |||
| SNPs as cofactors | SNP.9-1 | SNP.9-2 | MAF | ||||||
| SNP.9-1 | 1.00 | 2.0E-03 | 0.09 | (B2) North+East group | |||||
| SNP.9-2 | 4.2E-04 | 1.00 | 0.11 | SNPs as cofactors | SNP.3-3 | SNP.3-4 | SNP.3-6 | SNP.3-7a | MAF |
| SNP.3-3 | 1.00 | 0.79 | 0.36 | 0.09 | 0.28 | ||||
| (A3) West group | SNP.3-4 | 0.83 | 1.00 | 0.32 | 0.11 | 0.27 | |||
| SNPs as cofactors | SNP.9-1 | SNP.9-2 | MAF | SNP.3-6 | 0.48 | 0.45 | 1.00 | 0.33 | 0.45 |
| SNP.9-1 | 1.00 | 0.22 | 0.13 | SNP.3-7a | 0.16 | 0.21 | 0.28 | 1.00 | 0.33 (0.67)a |
| SNP.9-2 | 0.41 | 1.00 | 0.14 | ||||||
| (B3) West group | |||||||||
| (A4) South group | SNPs as cofactors | SNP.3-3 | SNP.3-4 | SNP.3-6 | SNP.3-7 | MAF | |||
| SNPs as cofactors | SNP.9-1 | SNP.9-2 | MAF | SNP.3-3 | 1.00 | 0.69 | 0.34 | 0.04 | 0.06 |
| SNP.9-1 | 1.00 | 0.07 | 0.09 | SNP.3-4 | 0.77 | 1.00 | 0.37 | 0.07 | 0.06 |
| SNP.9-2 | 0.06 | 1.00 | 0.05 | SNP.3-6 | 0.49 | 0.55 | 1.00 | 0.21 | 0.12 |
| SNP.3-7 | 0.09 | 0.12 | 0.21 | 1.00 | 0.39 | ||||
| (B4) South group | |||||||||
| SNPs as cofactors | SNP.3-3 | SNP.3-4 | SNP.3-6 | SNP.3-7 | MAF | ||||
| SNP.3-3 | 1.00 | 0.02 | 0.41 | 0.02 | 0.11 | ||||
| SNP.3-4 | 0.01 | 1.00 | 0.04 | 4.7E-03 | 0.01 | ||||
| SNP.3-6 | 0.43 | 0.07 | 1.00 | 0.03 | 0.13 | ||||
| SNP.3-7 | 0.03 | 0.02 | 0.04 | 1.00 | 0.17 | ||||
Values below the diagonal line refer to the usual r2 and above the diagonal line refer to (i.e., with correction for relatedness and population structure) MAF of the SNPs are given for the whole population and the three geographic groups.
The allele found in the North-East group with the lowest frequency at the SNP.3-7 was the opposite to the one that appeared in the lowest frequency in the whole population and the other two geographic groups.
Pairwise LD between SNPs are highlighted using the following color scale: red (r2 = 1) and yellow (r2 = 0).