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Table 2 Phenotype prediction accuracy based on genotype of selected trait-associated SNPs

From: Explore the genetics of weedy traits using rice 3K database

Trait Pop No. Ind SNP Genotype Freq Prediction accuracy
AWN aus 145 S6_7624195 AA 0.74 73.8% awn-less
     GG 0.26 68.4% awned
AWN trop 375 S8_24022229 GG 0.9 80.1% awn-less
     AA 0.1 89.1% awned
PTH trop 378 S7_13096799 GG 0.76 73.4% difficult (41.6%) to intermediate (31.8) threshing
     AA 0.23 90.9% easy (38.6%) to intermediate (52.2%) threshing
SCCO aus 153 S7_6068017 CC 0.68 96.1% colored seed coat
     AA 0.31 93.8% white seed coat
SCCO aus 153 S8_9105408 GG 0.65 86% colored seed coat
     AA 0.33 66.7% white seed coat
SCCO ind 645 S7_6067855 GG 0.92 96.1% white seed coat
     AA 0.07 91.5% colored seed coat
SCCO trop 362 S7_6062746 TT 0.9 90.5% white seed coat
     GG 0.1 88.9% colored seed coat
SDHT ind 641 S11_24872440 CC 0.85 92.1% short (21%) to intermediate (70%) seedling
     TT 0.13 95.2% intermediate (71%) to tall (23%) seedling
SDHT temp 137 S1_31283533 AA 0.75 62.1% short seedling
     GG 0.25 94% intermediate seedling
  1. The meaning for each trait abbreviation is as follows: AWN: awn color; PTH: panicle threshability, SCCO: seed coat color; SDHT: seedling height. Sub-population × trait combinations are shown in the table if the genotype of trait-associated SNP can predict the phenotype with at least 60% of chance to accuracy. Otherwise we do not present the Sub-population × trait combinations for a clear and concise presentation
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