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 mr1600 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
vg0431422103 sf0431237001 4 31422103 1.79E-08 7.30E-07
vg0904060062 sf0904059062 9 4060062 8.08E-08 3.06E-06
vg1016787143 sf1016715916 10 16787143 1.92E-07 9.05E-07
vg0827581531 sf0827578817 8 27581531 1.06E-06 4.58E-06
vg1106998620 sf1106994365 11 6998620 1.12E-06 4.51E-06
vg0901529324 sf0901528324 9 1529324 5.83E-06 NA
vg0814748323 sf0814745609 8 14748323 9.97E-06 8.69E-06