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 mr1544 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
vg0501722287 sf0501722271 5 1722287 2.52E-07 8.85E-08
vg0801866117 sf0801865120 8 1866117 3.23E-06 1.78E-06
vg1117621832 sf1117155688 11 17621832 5.36E-06 NA
vg0305017305 sf0305016307 3 5017305 NA 1.97E-06
vg0616489538 sf0616488540 6 16489538 NA 4.02E-06