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 mr1702 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
vg0119470291 sf0119469246 1 19470291 3.50E-07 3.49E-06
vg1019732665 sf1019661165 10 19732665 1.26E-06 5.00E-06
vg0601771504 sf0601770505 6 1771504 3.17E-06 3.27E-06
vg1019873752 sf1019802252 10 19873752 7.04E-06 1.96E-06
vg0911637912 sf0911636911 9 11637912 8.86E-06 4.70E-06
vg1004572532 sf1004589070 10 4572532 NA 5.37E-06