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
vg0400357479 sf0400356479 4 357479 1.73E-07 1.72E-07
vg1125315215 sf1124849055 11 25315215 8.31E-07 8.27E-07
vg0317023117 sf0317021991 3 17023117 2.86E-06 2.85E-06
vg0207676646 sf0207676646 2 7676646 2.86E-06 2.86E-06
vg1117140650 sf1116674502 11 17140650 4.72E-06 4.72E-06
vg1004688821 sf1004705358 10 4688821 8.69E-06 8.65E-06