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 mr1708 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
vg0127210847 sf0127209803 1 27210847 2.81E-29 2.38E-06
vg0910150356 sf0910149355 9 10150356 6.69E-28 NA
vg0229574749 sf0229568880 2 29574749 6.88E-28 NA
vg0819989626 sf0819986913 8 19989626 8.63E-28 6.16E-06
vg0332456370 sf0332449243 3 32456370 1.20E-27 NA
vg0702641922 sf0702640923 7 2641922 1.97E-27 7.03E-06
vg0610187834 sf0610186835 6 10187834 NA 2.42E-06