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 mr1758 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
vg1116008747 sf1115543619 11 16008747 5.79E-09 5.79E-09
vg1112695068 sf1112231389 11 12695068 2.06E-07 2.06E-07
vg0614107939 sf0614106940 6 14107939 8.87E-07 8.87E-07
vg1005205045 sf1005221582 10 5205045 1.52E-06 1.52E-06
vg1005203428 sf1005219965 10 5203428 2.76E-06 2.76E-06
vg1112624940 sf1112161143 11 12624940 2.85E-06 2.85E-06
vg1110902848 sf1110897165 11 10902848 4.50E-06 4.50E-06
vg1114989679 sf1114525993 11 14989679 4.72E-06 4.72E-06
vg1114666752 sf1114203070 11 14666752 4.84E-06 4.84E-06