Table 2. Locus pairs in significant (P<0.01) LD, r2 values and extent of LD in the two subgene pools.
| LG | Gene pool | No. Loci | No. (%) of locus pair in LD | Range (mean, median) of r2 | Extent (mean, median) of LD (cM) |
|---|---|---|---|---|---|
| 1 | SV | 38 | 77 (12.2) | 0.05–1 (0.40, 0.37) | 30 (8, 6.6) |
| NSV | 40 (6.3) | 0.03–1 (0.33, 0.24) | 57 (13.7, 2.5) | ||
| 2 | SV | 56 | 57 (3.7) | 0.02–1 (0.33, 0.21) | 61 (24, 27) |
| NSV | 151 (9.8) | 0.04–1 (0.33, 0.24) | 72 (13.5, 6.5) | ||
| 3 | SV | 76 | 204 (7.2) | 0.01–1 (0.28, 0.2) | 78 (23, 19) |
| NSV | 136 (4.8) | 0.02–0.9 (0.25–0.2) | 73 (14.4, 6.4) | ||
| 4 | SV | 30 | 28 (6.4) | 0.05–0.9 (0.29, 0.21) | 35 (9.9, 8) |
| NSV | 27 (6.2) | 0.06–0.87 (0.29, 0.24) | 27 (6.2, 3.3) | ||
| 5 | SV | 28 | 62 (16.4) | 0.12–1 (0.57, 0.54) | 50 (11, 9.5) |
| NSV | 21 (5.6) | 0.09–1 (0.4, 0.39) | 38 (6.4, 1.2) | ||
| 6 | SV | 41 | 38 (4.6) | 0.12–1 (0.48, 0.44) | 42 (9.8, 7.3) |
| NSV | 67 (8.2) | 0.04–0.9 (0.3, 0.25) | 64 (17.3, 11.8) | ||
| 7 | SV | 32 | 71 (14.3) | 0.06–0.9 (0.4, 0.31) | 26 (10, 7.5) |
| NSV | 23 (4.6) | 0.04–0.6 (0.3, 0.26) | 32 (7.3, 0.6) | ||
| 8 | SV | 27 | 35 (10) | 0.21–1 (0.53, 0.48) | 37 (10.6, 6.9) |
| NSV | 32 (9.1) | 0.06–0.9 (0.39, 0.34) | 42 (5.1, 1.1) | ||
| 9 | SV | 36 | 39 (6.2) | 0.15–1 (0.46, 0.38) | 40 (12.7, 10) |
| NSV | 36 (5.7) | 0.02–1 (0.26, 0.17) | 29 (9.2, 6) | ||
| 10 | SV | 23 | 17 (6.7) | 0.05–0.95 (0.4, 0.36) | 42 (17.8, 8.8) |
| NSV | 13 (5.1) | 0.06–0.87 (0.4, 0.37) | 24 (4.4, 1.1) | ||
| 11 | SV | 28 | 71 (18.8) | 0.06–0.9 (0.46, 0.33) | 31 (7, 10) |
| NSV | 48 (12.7) | 0.18–0.87 (0.7, 0.86) | 13 (1.2, 0.5) | ||
| Genome-wide | SV | 415 | 3937 (4.6)a | 0.01–1 (0.39, 0.3) | 78 (15, 9.5) |
| NSV | 2909 (3.4)a | 0.02–1 (0.34, 0.27) | 66 (11.2, 3.5) |
Abbreviations: NSV, non-standard vegetable; SV, standard vegetable.
a
The numbers and proportions of locus pairs in linkage disequilibrium (LD) on the whole genome scale includes both intrachromosomal and interchromosomal associations.