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
vg0222736681 sf0222730812 2 22736681 3.94E-12 3.86E-11
vg0900499731 sf0900498731 9 499731 2.36E-08 1.63E-06
vg1207863655 sf1207861061 12 7863655 2.99E-08 4.96E-07
vg0331768637 sf0331761514 3 31768637 4.91E-08 NA
vg0809461403 sf0809460407 8 9461403 5.51E-06 3.45E-06
vg0312535741 sf0312534459 3 12535741 6.62E-06 NA