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 mr1703 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
vg1014673851 sf1014602617 10 14673851 8.75E-07 8.75E-07
vg0119643493 sf0119642448 1 19643493 1.05E-06 1.05E-06
vg1014419290 sf1014348056 10 14419290 1.83E-06 1.83E-06
vg0311427500 sf0311426218 3 11427500 1.90E-06 1.90E-06
vg0103300358 sf0103299358 1 3300358 2.53E-06 2.53E-06