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 mr1714 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
vg0206494550 sf0206494550 2 6494550 2.40E-08 2.40E-08
vg0206092855 sf0206092855 2 6092855 1.64E-06 1.64E-06
vg0401652221 sf0401647770 4 1652221 2.52E-06 2.52E-06
vg0209742252 sf0209742250 2 9742252 3.61E-06 3.61E-06
vg1115974964 sf1115509836 11 15974964 3.85E-06 3.85E-06
vg1203668850 sf1203667849 12 3668850 5.51E-06 5.51E-06