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 mr1105 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
vg0526213742 sf0526151106 5 26213742 8.56E-42 1.38E-06
vg0526297588 sf0526234951 5 26297588 1.42E-40 4.83E-07
vg1225940329 sf1225906723 12 25940329 2.31E-40 NA
vg0303208453 sf0303207449 3 3208453 1.04E-39 NA
vg0303210296 sf0303209292 3 3210296 1.68E-39 NA
vg0221191695 sf0221185827 2 21191695 5.41E-39 NA
vg0619618492 sf0619617495 6 19618492 8.37E-39 NA
vg0132063180 sf0132062136 1 32063180 NA 1.61E-06
vg0807773496 sf0807772500 8 7773496 NA 3.02E-06
vg0918922771 sf0918921771 9 18922771 NA 8.78E-06