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 mr1235 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
vg0216649473 sf0216643603 2 16649473 8.34E-18 2.25E-08
vg0417021326 sf0416849368 4 17021326 5.20E-14 NA
vg1018577737 sf1018506294 10 18577737 5.39E-14 NA
vg0906644203 sf0906643203 9 6644203 1.44E-13 NA
vg0516032137 sf0515974645 5 16032137 3.50E-13 NA
vg0813447304 sf0813444857 8 13447304 1.48E-11 2.72E-06