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 mr1756 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
vg0403573729 sf0403569330 4 3573729 1.97E-06 1.97E-06
vg0219767723 sf0219761855 2 19767723 2.22E-06 2.22E-06
vg1010927325 sf1010856145 10 10927325 3.55E-06 3.55E-06
vg0431034778 sf0430849662 4 31034778 3.59E-06 3.59E-06
vg1207699197 sf1207696601 12 7699197 4.85E-06 4.85E-06
vg0610531602 sf0610530603 6 10531602 9.01E-06 9.01E-06