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Table 1 Trait-associated SNP identified within each sub-population of 3K-RGP

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 7.23E08 21   
  aus S4_4462447 2.33E07 21   
  temp S4_4464494 1.28E07 21   
  aus S4_4488660 9.51E08 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 3.98E54 15 Os07g0211500 (-0.1 kb) Rc
  ind S7_6067855 1.15E114 15 Os07g0211500 Rc
  aus S7_6068017 1.81E40 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   
  1. The meaning for each trait abbreviation is as follows: AWCO_REV: awn color; PSH: panicle shattering degree; PTH: panicle threshability, SCCO_REV: seed coat color; SDHT_CODE: seedling height. Pop: sub-populations, including aus, indica (ind), temperate japonica (temp), and tropical japonica (trop). Markers were named based on their genomic position on the reference sequence (cv Nipponbarre, IRGSP v1) for S[chromosome]_[bp position on the chromosome]. When the trait-associated SNP fell into an annotated gene, the gene name was indicated in the column of “Candidate gene”. If a gene, whose function was related to the trait of interest, fell within ± 100 kb of the trait-associated SNP, the distance between the SNP and the start of the gene is indicated in the parentheses: minus sign means before the SNP, plus sign means after the SNP. Annotation was from RAP-DB. Closely positioned SNPs for which the same genes were identified within the ± 100 kb region were underlined in bold
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