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 mr1706 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
vg0128562860 sf0128561815 1 28562860 4.80E-11 7.22E-06
vg0141382072 sf0141381029 1 41382072 1.03E-08 NA
vg0621044029 sf0621043032 6 21044029 2.07E-08 6.62E-06
vg0922222774 sf0922222293 9 22222774 3.19E-08 NA
vg1022972787 sf1022901259 10 22972787 4.08E-08 NA
vg0300353676 sf0300352674 3 353676 3.88E-07 NA
vg0303087401 sf0303086397 3 3087401 7.41E-07 NA
vg0107999218 sf0107998218 1 7999218 1.22E-06 NA
vg1113127527 sf1112663848 11 13127527 1.41E-06 NA
vg1223038282 sf1223004742 12 23038282 6.24E-06 5.11E-06