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 mr1092 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
vg0130670983 sf0130669939 1 30670983 9.03E-11 8.36E-08
vg0103512299 sf0103511299 1 3512299 2.20E-10 NA
vg1203606223 sf1203605222 12 3606223 6.86E-09 NA
vg0805562556 sf0805561559 8 5562556 3.12E-08 NA
vg0306207246 sf0306206246 3 6207246 6.17E-08 NA
vg0628170354 sf0628169356 6 28170354 9.92E-07 NA