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 mr1356 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
vg1122514350 sf1122048221 11 22514350 2.96E-08 2.97E-08
vg1218022533 sf1217993969 12 18022533 1.77E-07 1.77E-07
vg1218074718 sf1218046154 12 18074718 5.82E-07 5.82E-07
vg1013275525 sf1013204295 10 13275525 8.64E-07 8.64E-07
vg1117596956 sf1117130813 11 17596956 2.04E-06 2.03E-06
vg1218421558 sf1218392994 12 18421558 2.62E-06 2.62E-06