Table 3.
Quantitative trait loci (QTL) for grain size in the F2 and F2:3 populations from the cross ZS97/Egy316
| Trait | QTL | Interval (bp) | F2 | F2:3 | Neighbor gene | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| LOD | A | D | PVE % | LOD | A | D | PVE % | ||||
| GL | qGL1.1 | chr01_6252160-6528362 | 2.7 | − 0.06 | −0.11 | 2.7 | 2.5 | −0.22 | −0.41 | 2.3 | |
| qGL1.2 | chr01_36420775-36829167 | 9.9 | 0.25 | 0.11 | 10.9 | 3.1 | 0.31 | −0.11 | 2.6 | ||
| qGL2.1 | chr02_24836231-25154458 | 3.3 | 0.11 | −0.50 | 2.4 | ||||||
| qGL3.1 | chr03_16285838-16886243 | 26.6 | 0.36 | −0.31 | 22.1 | 23 | 0.42 | −0.11 | 19.2 | −0.4 Mb to GS3 | |
| qGL4.1 | chr04_22263737-22639082 | 3.3 | 0.11 | −0.03 | 2.9 | ||||||
| qGL4.2 | chr04_33536150-33674756 | 2.5 | −0.07 | −0.09 | 2.6 | ||||||
| qGL5.1 | chr05_22523494-22643495 | 4.7 | 0.11 | −0.11 | 3.8 | ||||||
| qGL6.1 | chr06_1-721973 | 3.9 | 0.14 | −0.01 | 3.1 | 3.7 | 0.12 | −0.02 | 4.4 | ||
| qGL6.2 | chr06_28042873-28197236 | 5.7 | 0.15 | 0.01 | 4.6 | 6.1 | 0.11 | 0.12 | 6.8 | ||
| qGL7.1 | chr07_22710399-22852604 | 6.6 | 0.29 | 0.19 | 6.3 | ||||||
| qGL10.1 | chr10_22826960-23064487 | 7.9 | −0.21 | −0.01 | 9.1 | 3.6 | −0.11 | −0.04 | 5.6 | ||
| qGL11.1 | chr11_22000836-22382239 | 6.8 | 0.30 | 0.11 | 3.9 | ||||||
| GW | qGW1.1 | chr01_40061411-40232403 | 23 | 0.21 | 0.07 | 16.2 | 2.8 | 0.14 | 0.12 | 3.2 | |
| qGW2.1 | chr02_8624971-8785185 | 5.1 | 0.05 | 0.04 | 7.2 | 7.1 | 0.16 | 0.08 | 5 | +0.5 Mb to GW2 | |
| qGW2.2 | chr02_23227105-23395836 | 7.1 | 0.16 | 0.08 | 5.1 | ||||||
| qGW3.1 | chr03_27774267-28044025 | 2.6 | 0.06 | −0.15 | 3.5 | 4.1 | 0.06 | −0.29 | 6.2 | ||
| qGW4.1 | chr04_34347387-34635947 | 2.5 | −0.04 | 0.11 | 2 | 4.3 | −0.12 | 0.18 | 5.2 | ||
| qGW5.1 | chr05_4872672-5032093 | 19.1 | −0.15 | −0.02 | 16.3 | 16.7 | −0.19 | 0.11 | 10.2 | −0.4 Mb to GW5 | |
| qGW6.1 | chr06_4804633-4979917 | 4.1 | −0.01 | −0.11 | 3.3 | 10.7 | −0.19 | 0.11 | 8.3 | ||
| qGW6.2 | chr06_26495233-26725102 | 4.1 | 0.13 | 0.15 | 3.2 | ||||||
| qGW10.1 | chr10_23724974-23956998 | 2.8 | −0.06 | −0.12 | 2.8 | 6.7 | −1.11 | −0.18 | 3.1 | ||
| TGW | qTGW1.1 | chr01_39735532-40061411 | 16 | 3.41 | 2.81 | 7.5 | 5.8 | 0.15 | 1.51 | 2.5 | |
| qTGW2.1 | chr02_27175409-27295409 | 2.9 | 1.31 | 0.71 | 3.9 | 6.5 | 1.10 | 0.21 | 2.9 | ||
| qTGW3.1 | chr03_20243818-20710332 | 3.5 | 0.81 | −0.32 | 2.5 | ||||||
| qTGW4.1 | chr04_33674756-33842888 | 2.7 | −0.50 | −0.61 | 2.1 | ||||||
| qTGW5.1 | chr05_17173895-17293895 | 4.1 | −1.91 | 0.52 | 5.9 | 5.8 | −1.32 | 0.41 | 5.8 | ||
| qTGW10.1 | chr10_23064487-23314589 | 9.3 | −1.50 | 0.04 | 5.5 | ||||||
Traits: GL, grain length (mm); GW, grain width (mm); and TGW, thousand-grain weight (g). Interval, location of quantitative trait loci (QTLs) on chromosome by bp; LOD, logarithm of odds; A, additive effect; D, Dominance effect and PVE (%), the phenotypic variance explained by each QTL. Position of neighbor genes according to The Rice Annotation Project Database