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 mr1766 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
vg1121372738 sf1120906615 11 21372738 6.53E-09 6.53E-09
vg1120930814 sf1120464717 11 20930814 2.18E-08 2.18E-08
vg1002401537 sf1002400514 10 2401537 4.27E-07 4.27E-07
vg1127383071 sf1126911458 11 27383071 8.80E-07 8.80E-07
vg0142197597 sf0142196553 1 42197597 2.05E-06 2.05E-06
vg0828226493 sf0828223779 8 28226493 4.12E-06 4.12E-06