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 mr1500 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
vg0314910245 sf0314908892 3 14910245 7.01E-08 6.25E-07
vg1221741274 sf1221707821 12 21741274 2.11E-07 2.41E-06
vg0624472081 sf0624471084 6 24472081 4.46E-07 1.03E-06
vg0411387439 sf0411378142 4 11387439 1.01E-06 2.85E-06
vg0105133448 sf0105132448 1 5133448 3.63E-06 3.37E-06
vg1104596397 sf1104592299 11 4596397 NA 8.02E-07
vg0815186428 sf0815183714 8 15186428 NA 1.63E-06
vg0918726676 sf0918725676 9 18726676 NA 3.97E-06