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 mr1303 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
vg1117464587 sf1116998442 11 17464587 6.80E-07 6.81E-07
vg0412949354 sf0412940065 4 12949354 1.24E-06 1.24E-06
vg0321991817 sf0321990324 3 21991817 1.49E-06 1.49E-06
vg0406883539 sf0406878798 4 6883539 3.95E-06 3.95E-06
vg0726576732 sf0726575738 7 26576732 4.59E-06 4.59E-06