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 mr1012 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
vg0139415631 sf0139414588 1 39415631 7.62E-07 7.61E-07
vg0622249479 sf0622248482 6 22249479 1.70E-06 1.70E-06
vg0616238331 sf0616237333 6 16238331 2.73E-06 2.73E-06
vg0622187287 sf0622186290 6 22187287 3.61E-06 3.61E-06
vg0112129025 sf0112127999 1 12129025 4.44E-06 4.44E-06