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 mr1808 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
vg0520706309 sf0520643750 5 20706309 2.50E-12 9.58E-06
vg0133325596 sf0133324552 1 33325596 5.85E-12 3.91E-07
vg0918268132 sf0918267131 9 18268132 1.51E-11 8.40E-06
vg0804856202 sf0804855205 8 4856202 4.72E-11 NA
vg0528508567 sf0528445922 5 28508567 5.92E-11 NA