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 mr1809 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
vg1117584893 sf1117118750 11 17584893 5.50E-08 5.50E-08
vg0504650681 sf0504650658 5 4650681 3.32E-06 3.32E-06
vg1119202979 sf1118736667 11 19202979 3.40E-06 3.40E-06
vg1127125428 sf1126653815 11 27125428 3.59E-06 3.59E-06
vg0329591528 sf0329584568 3 29591528 4.40E-06 4.40E-06