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 mr1883 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
vg0208440052 sf0208440051 2 8440052 1.05E-07 1.05E-07
vg0420699382 sf0420527425 4 20699382 1.86E-07 1.86E-07
vg0401115443 sf0401110993 4 1115443 3.69E-06 3.69E-06
vg0500551214 sf0500551214 5 551214 3.91E-06 3.92E-06
vg0722706364 sf0722705371 7 22706364 5.62E-06 5.62E-06