Table 2.
QTLs for shoot regeneration traits (Bud percentage (B), Regeneration percentage (R) and Productivity Rate (PR)) found to be significant at the empirical genome wide mapping threshold by restricted Multiple QTL Mapping (rMQM) in BC1 and Interval Mapping (IM) in F2
| Test | QTL analysis | Trait | QTL | Genome wide significant threshold level (P < 0.05) | Chr | Start (cM) |
Finish (cM) |
Coverage (cM) | LOD Peak | Position of LOD peak (cM) | Peak marker a | %variance explained | Estimated additive effect | Estimated dominance effect |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BC1 | rMQM | B | SpRg-1 | 2.7 | 1 | 3.87 | 44.42 | 40.55 | 7.12 | 22.47 | C2_At1g65520/C2_At2g45910 | 23.9 | -31.56 | |
| BC1 | rMQM | R | SpRg-1 | 2.7 | 1 | 3.87 | 43.42 | 39.55 | 5.52 | 24.47 | C2_At1g65520/C2_At2g45910 | 15.0 | -24.10 | |
| BC1 | rMQM | PR | SpRg-1 | 2.8 | 1 | 3.87 | 34.42 | 30.55 | 4.19 | 22.47 | C2_At1g65520/C2_At2g45910 | 10.2 | -0.70 | |
| BC1 | rMQM | B | Rg-3 | 2.7 | 3 | 42.41 | 55.80 | 13.39 | 4.64 | 50.47 | ME20-199 | 12.2 | -21.60 | |
| BC1 | rMQM | PR | Rg-3 | 2.8 | 3 | 32.77 | 63.10 | 30.33 | 4.26 | 50.47 | ME20-199 | 10.6 | -0.68 | |
| BC1 | rMQM | R | SpRg-4a | 2.7 | 4 | 44.39 | 61.24 | 16.85 | 4.94 | 50.24 | TAHINA-4-71, 3 | 13.3 | -22.29 | |
| BC1 | rMQM | PR | SpRg-4b | 2.8 | 4 | 81.33 | 93.18 | 11.85 | 3.08 | 86.33 | SSR214/SSR146 | 7.4 | -0.63 | |
| F2 | IM | B | SpRg-7 | 3.7 | 7 | 2.20 | 40.28 | 38.08 | 6.84 | 19.51 | ME10-141/C2_At4g26680 | 27.0 | -22.20 | 12.32 |
| F2 | IM | R | SpRg-7 | 3.6 | 7 | 4.50 | 40.28 | 35.78 | 6.18 | 19.51 | ME10-141/C2_At4g26680 | 24.8 | -23.29 | 13.63 |
| F2 | IM | PR | SpRg-7 | 4.4 | 7 | 19.51 | 36.28 | 16.77 | 5.72 | 28.28 | C2_At1g17200 | 23.1 | -1.53 | -0.55 |
| BC1 | rMQM | R | SpRg-7 | 2.7 | 7 | 0.00 | 25.08 | 25.08 | 5.47 | 13.44 | TAHINA-7-43 | 14.9 | -23.13 | |
| BC1 | rMQM | PR | SpRg-7 | 2.8 | 7 | 3.54 | 28.23 | 24.69 | 5.28 | 13.44 | TAHINA-7-43 | 13.5 | -0.77 | |
| BC1 | rMQM | B | SpRg-8 | 2.7 | 8 | 41.18 | 53.37 | 12.19 | 3.84 | 46.37 | C2_At1g64150 | 12.2 | 21.25 | |
| BC1 | rMQM | R | SpRg-8 | 2.7 | 8 | 42.18 | 58.90 | 16.72 | 4.25 | 53.37 | C2_At1g64150/C2_At4g23840 | 9.3 | 19.35 | |
aIn case of the absence of a peak marker, loci flanking the likely peak of a QTL are shown.