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 mr1125 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
vg0235337136 sf0235331267 2 35337136 8.25E-14 3.70E-11
vg0235365192 sf0235359323 2 35365192 2.92E-11 4.85E-09
vg1108660993 sf1108655603 11 8660993 1.53E-09 2.91E-07
vg1125670940 sf1125204779 11 25670940 4.49E-09 9.33E-07
vg0203671161 sf0203671158 2 3671161 6.28E-09 1.57E-06
vg1114018010 sf1113554331 11 14018010 6.94E-09 1.89E-06
vg0914935450 sf0914934449 9 14935450 2.06E-08 2.62E-06
vg0523767761 sf0523705182 5 23767761 2.68E-08 1.18E-06
vg0815679964 sf0815677250 8 15679964 3.50E-08 7.52E-06
vg0805055259 sf0805054262 8 5055259 NA 1.64E-06
vg0918671171 sf0918670170 9 18671171 NA 2.00E-06