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 mr1600 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
vg0222739831 sf0222733962 2 22739831 7.30E-16 1.07E-15
vg0222725881 sf0222720012 2 22725881 1.60E-15 9.13E-16
vg0610750218 sf0610749219 6 10750218 3.88E-08 8.81E-06
vg0705335233 sf0705334234 7 5335233 7.24E-08 NA
vg0608528871 sf0608527872 6 8528871 9.21E-07 4.46E-06
vg0131880868 sf0131879824 1 31880868 7.02E-06 4.57E-06