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 mr1991 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
vg1220793576 sf1220760124 12 20793576 5.28E-21 3.09E-16
vg1224806805 sf1224773259 12 24806805 7.89E-13 7.21E-08
vg0216615136 sf0216609266 2 16615136 1.93E-10 NA
vg0620227512 sf0620226515 6 20227512 2.06E-10 NA
vg0824279038 sf0824276324 8 24279038 5.05E-10 2.82E-06
vg1220129699 sf1220101141 12 20129699 NA 1.04E-06