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 mr1053 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
vg0805068294 sf0805067297 8 5068294 5.19E-07 5.19E-07
vg0722226606 sf0722225613 7 22226606 2.31E-06 2.31E-06
vg1214703763 sf1214701104 12 14703763 2.33E-06 2.33E-06
vg0918774898 sf0918773898 9 18774898 2.57E-06 2.57E-06
vg1204324619 sf1204323607 12 4324619 3.21E-06 3.21E-06