From: Explore the genetics of weedy traits using rice 3K database
Trait | Pop | SNP | P-value | No. gene ± 100 kb | Candidate genes | Annotation |
---|---|---|---|---|---|---|
AWCO_REV | ind | S1_2222938 | 2.34E−08 | 19 | ||
temp | S1_26642467 | 1.64E−09 | 18 | |||
temp | S1_34999638 | 6.77E−07 | 25 | Os01g0820700 | OsWRKY116 | |
ind | S1_38893251 | 1.26E−07 | 32 | Os01g0894500 | Sep15/SelM redox domain containing protein | |
aus | S2_5126277 | 1.35E−08 | 36 | |||
aus | S2_18016425 | 3.79E−08 | 15 | |||
ind | S2_20021623 | 3.27E−07 | 19 | |||
aus | S2_35221348 | 1.99E−07 | 42 | |||
aus | S3_14604626 | 7.34E−08 | 26 | |||
trop | S3_22066093 | 1.37E−08 | 22 | |||
temp | S4_3569126 | 8.05E−10 | 13 | |||
ind | S4_32368836 | 9.04E−09 | 40 | Os04g0636500 | BTB domain containing protein | |
trop | S5_23650885 | 3.36E−07 | 30 | |||
aus | S6_7624195 | 3.23E−10 | 25 | |||
trop | S6_21261276 | 1.08E − 11 | 19 | |||
ind | S6_22232682 | 2.78E−07 | 25 | |||
aus | S7_671056 | 2.97E−08 | 27 | |||
ind | S7_8538306 | 1.93E−08 | 8 | Os07g0253100 | Conserved hypothetical protein | |
ind | S7_27892037 | 1.19E−09 | 36 | |||
temp | S8_23747966 | 2.51E−07 | 22 | |||
trop | S8_24022229 | 7.43E−12 | 37 | Os08g0485800 | Barwin-related endoglucanase domain containing protein | |
Os08g0485500 (− 23.4 kb) | RAE2; Regulation of awn development and elongation | |||||
ind | S10_10954998 | 1.67E−08 | 16 | |||
trop | S12_14872482 | 1.84E−11 | 11 | |||
PSH | temp | S2_18492267 | 1.99E−07 | 19 | ||
temp | S3_3398933 | 1.35E−08 | 34 | |||
aus | S4_4462336 | 7.23E−08 | 21 | |||
aus | S4_4462447 | 2.33E−07 | 21 | |||
temp | S4_4464494 | 1.28E−07 | 21 | |||
aus | S4_4488660 | 9.51E−08 | 21 | Os04g0166000 | Conserved hypothetical protein | |
temp | S4_5387818 | 4.08E−07 | 10 | |||
temp | S12_1917244 | 5.88E−08 | 35 | Os12g0139400 | OsRR10 | |
PTH | trop | S2_24505237 | 1.22E−07 | 23 | ||
trop | S7_13096799 | 5.14E−12 | 12 | |||
trop | S8_20373414 | 1.06E−10 | 20 | |||
SCCO_REV | ind | S1_8264505 | 2.21E−07 | 30 | ||
ind | S1_14709154 | 2.38E−14 | 18 | |||
ind | S1_19343008 | 2.26E−07 | 18 | |||
trop | S2_20541410 | 5.66E−08 | 10 | |||
ind | S2_35121783 | 1.35E−07 | 34 | Os02g0818700 | Similar to tumor-related protein | |
temp | S3_4766628 | 8.81E−07 | 36 | |||
temp | S3_12419022 | 3.69E−09 | 32 | |||
trop | S3_16978020 | 4.30E−07 | 18 | |||
aus | S3_29290186 | 4.03E−08 | 20 | |||
trop | S7_6062746 | 3.98E−54 | 15 | Os07g0211500 (-0.1 kb) | Rc | |
ind | S7_6067855 | 1.15E−114 | 15 | Os07g0211500 | Rc | |
aus | S7_6068017 | 1.81E−40 | 15 | Os07g0211500 | Rc | |
temp | S7_23073822 | 7.43E−15 | 29 | Os07g0571500 | Similar to transmembrane protein 49 | |
ind | S8_8581885 | 1.39E−08 | 15 | |||
aus | S8_9105408 | 4.44E−11 | 22 | Os08g0249100 | OsRLCK249 | |
ind | S9_1298020 | 2.85E−08 | 14 | |||
temp | S10_10394027 | 1.15E−08 | 13 | Os10g0346300 | OsLAC17 | |
trop | S11_17682735 | 8.45E−09 | 10 | |||
trop | S11_19853800 | 6.99E−08 | 12 | |||
SDHT_CODE | aus | S1_15921134 | 1.38E−07 | 11 | ||
aus | S1_30508051 | 1.69E−08 | 37 | |||
temp | S1_31283533 | 4.33E−07 | 27 | |||
ind | S2_19154582 | 8.69E−08 | 19 | |||
aus | S2_19678534 | 3.74E−08 | 24 | |||
aus | S4_21716120 | 1.96E−07 | 35 | |||
ind | S8_8643208 | 4.52E−13 | 11 | |||
ind | S8_25508381 | 2.02E−09 | 25 | Os08g0242400 (-2.4 kb) | OsWOX10 | |
ind | S11_20514671 | 4.20E−11 | 20 | Os11g0551900 (+7.3 kb) | OsGRF8 | |
ind | S11_24872440 | 2.62E−11 | 12 | |||
aus | S12_154948 | 4.55E−08 | 26 | |||
ind | S12_365399 | 6.12E−08 | 34 | |||
ind | S12_25154542 | 2.89E−11 | 26 |