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 mr1220 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
vg0610251688 sf0610250689 6 10251688 1.79E-09 7.12E-06
vg0706070366 sf0706069367 7 6070366 5.02E-09 NA
vg0610087325 sf0610086326 6 10087325 1.04E-08 2.73E-06
vg0719512195 sf0719511202 7 19512195 4.67E-08 NA
vg0912341415 sf0912340414 9 12341415 4.69E-08 NA
vg0121758038 sf0121756993 1 21758038 6.03E-06 NA