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 mr1031 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
vg1208472138 sf1208469545 12 8472138 5.17E-14 1.67E-06
vg0433930554 sf0433745450 4 33930554 1.41E-12 1.79E-08
vg0304183946 sf0304182948 3 4183946 8.84E-12 NA
vg0304169062 sf0304168064 3 4169062 1.55E-11 NA
vg0529082765 sf0529020120 5 29082765 6.72E-11 NA
vg1217492814 sf1217486769 12 17492814 7.59E-11 NA
vg0433939228 sf0433754124 4 33939228 NA 6.45E-07
vg0121045975 sf0121044930 1 21045975 NA 1.79E-06