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 mr1115 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
vg0604294396 sf0604293397 6 4294396 3.65E-29 2.92E-12
vg0326933756 sf0326926809 3 26933756 1.53E-22 4.29E-07
vg0311232363 sf0311231081 3 11232363 3.26E-20 NA
vg1118381722 sf1117915582 11 18381722 5.88E-20 NA
vg0805092111 sf0805091114 8 5092111 5.71E-19 NA