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 mr1704 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
vg0820969276 sf0820966563 8 20969276 3.46E-07 3.46E-07
vg0817796326 sf0817793613 8 17796326 2.45E-06 2.45E-06
vg0421031231 sf0420859284 4 21031231 2.71E-06 2.71E-06
vg1109631523 sf1109626100 11 9631523 3.35E-06 3.35E-06
vg1109628487 sf1109623064 11 9628487 4.78E-06 4.78E-06