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
vg1211097492 sf1211094858 12 11097492 1.42E-12 NA
vg0305905056 sf0305904056 3 5905056 7.02E-12 NA
vg1213729703 sf1213727041 12 13729703 1.24E-11 NA
vg0329856598 sf0329849637 3 29856598 1.47E-11 NA
vg0805685577 sf0805684580 8 5685577 7.24E-11 NA
vg1022972787 sf1022901259 10 22972787 5.57E-09 4.88E-06
vg0205296507 sf0205296506 2 5296507 5.37E-08 3.07E-06
vg0620149436 sf0620148439 6 20149436 1.35E-07 NA
vg1004032949 sf1004031925 10 4032949 NA 8.18E-07
vg0520616960 sf0520554401 5 20616960 NA 8.63E-06