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 mr1655 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
vg0220269530 sf0220263662 2 20269530 4.06E-07 4.06E-07
vg0334658706 sf0334651576 3 34658706 1.21E-06 1.21E-06
vg1101663368 sf1101662369 11 1663368 1.55E-06 1.55E-06
vg1112971005 sf1112507326 11 12971005 2.82E-06 2.82E-06
vg0102255943 sf0102254943 1 2255943 3.06E-06 3.06E-06