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 mr1400 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
vg0111811184 sf0111810158 1 11811184 1.28E-06 7.04E-08
vg0111822580 sf0111821554 1 11822580 1.48E-06 8.04E-08
vg0223644159 sf0223638290 2 23644159 7.30E-06 1.42E-06
vg0111818505 sf0111817479 1 11818505 NA 1.56E-07
vg0708708061 sf0708707066 7 8708061 NA 7.75E-06