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 mr1746 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
vg0800287831 sf0800286831 8 287831 6.14E-39 1.21E-28
vg0800302779 sf0800301779 8 302779 1.38E-28 2.58E-21
vg0800324457 sf0800323457 8 324457 1.36E-26 4.96E-20
vg0223585784 sf0223579915 2 23585784 2.22E-12 8.05E-07
vg0223574312 sf0223568443 2 23574312 1.17E-11 3.78E-06
vg0800452763 sf0800451763 8 452763 2.73E-11 5.05E-08
vg0800345996 sf0800344996 8 345996 8.06E-11 1.04E-07
vg0800347061 sf0800346061 8 347061 1.47E-10 9.09E-08
vg0800272674 sf0800271674 8 272674 3.84E-10 4.08E-06
vg0800085930 sf0800084930 8 85930 3.26E-09 2.67E-07
vg0416940273 sf0416768315 4 16940273 3.27E-08 3.72E-07
vg1219719232 sf1219690702 12 19719232 9.32E-08 2.04E-07
vg1014151655 sf1014080421 10 14151655 NA 1.56E-06