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 mr1590 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
vg1218068231 sf1218039667 12 18068231 3.21E-07 6.52E-07
vg0312535741 sf0312534459 3 12535741 7.19E-07 2.69E-06
vg0129100082 sf0129099037 1 29100082 1.53E-06 7.31E-07
vg1216970927 sf1216964881 12 16970927 2.54E-06 2.41E-06
vg0315818548 sf0315817195 3 15818548 NA 3.79E-06