Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1509 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg1020493947 sf1020422426 10 20493947 2.67E-66 6.74E-15
vg1020420315 sf1020348794 10 20420315 2.81E-66 9.90E-16
vg0129959121 sf0129958076 1 29959121 8.99E-52 NA
vg0324070014 sf0324068093 3 24070014 6.01E-51 NA
vg0704675216 sf0704674217 7 4675216 1.68E-50 NA
vg0332643360 sf0332636231 3 32643360 2.45E-50 NA
vg0122331148 sf0122330103 1 22331148 NA 1.91E-07
vg0410227364 sf0410218061 4 10227364 NA 1.13E-06
vg0142242102 sf0142241058 1 42242102 NA 2.21E-06
vg0221436059 sf0221430191 2 21436059 NA 2.46E-06
vg0612813818 sf0612812819 6 12813818 NA 3.04E-06
vg1124474270 sf1124008110 11 24474270 NA 3.37E-06
vg1208765892 sf1208763299 12 8765892 NA 3.78E-06
vg1124474136 sf1124007976 11 24474136 NA 3.94E-06
vg0914907095 sf0914906094 9 14907095 NA 4.41E-06
vg0233244719 sf0233238850 2 33244719 NA 4.70E-06
vg0208558888 sf0208558887 2 8558888 NA 4.94E-06