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 mr1800 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
vg0432425185 sf0432240076 4 32425185 1.35E-11 1.34E-09
vg0432426919 sf0432241810 4 32426919 2.15E-11 1.12E-09
vg1117624908 sf1117158764 11 17624908 2.65E-10 6.44E-08
vg1118146962 sf1117680820 11 18146962 2.75E-06 4.73E-06
vg1204092989 sf1204091977 12 4092989 4.14E-06 4.50E-06
vg1119795272 sf1119337412 11 19795272 5.42E-06 2.98E-06
vg0622592636 sf0622591639 6 22592636 8.70E-06 2.17E-06