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 mr1344 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
vg0207854825 sf0207854824 2 7854825 1.05E-07 1.05E-07
vg1112983960 sf1112520281 11 12983960 1.61E-07 1.61E-07
vg1109628487 sf1109623064 11 9628487 1.88E-06 1.88E-06
vg0130689494 sf0130688450 1 30689494 2.13E-06 2.13E-06
vg0116961602 sf0116960556 1 16961602 2.38E-06 2.38E-06