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
vg0726584856 sf0726583862 7 26584856 6.70E-07 3.17E-06
vg0419095970 sf0418924008 4 19095970 8.77E-07 NA
vg0301371527 sf0301370525 3 1371527 1.42E-06 NA
vg0610852694 sf0610851695 6 10852694 2.76E-06 3.89E-06
vg1214302244 sf1214299584 12 14302244 7.40E-06 7.34E-06