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 mr1505 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
vg0131417081 sf0131416037 1 31417081 2.44E-08 7.74E-06
vg0431515534 sf0431330433 4 31515534 4.52E-08 1.50E-06
vg0820144025 sf0820141312 8 20144025 5.09E-08 9.18E-06
vg0821751104 sf0821748391 8 21751104 1.61E-06 1.81E-06
vg0608151572 sf0608150573 6 8151572 2.53E-06 NA
vg0317321849 sf0317320659 3 17321849 NA 6.75E-08
vg0106187082 sf0106186082 1 6187082 NA 3.22E-06
vg1214674928 sf1214672267 12 14674928 NA 4.11E-06