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 mr1441 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
vg0222725881 sf0222720012 2 22725881 1.28E-52 1.19E-26
vg0800545388 sf0800544388 8 545388 2.04E-19 NA
vg0716448920 sf0716447927 7 16448920 1.26E-18 NA
vg1203725293 sf1203724292 12 3725293 2.12E-18 NA
vg0701937367 sf0701936368 7 1937367 4.80E-18 NA
vg0222725003 sf0222719134 2 22725003 1.40E-17 1.03E-11
vg0222857256 sf0222851387 2 22857256 3.31E-15 1.60E-07
vg0221010404 sf0221004536 2 21010404 1.21E-13 NA
vg0705527867 sf0705526868 7 5527867 2.39E-13 NA
vg0123407656 sf0123406612 1 23407656 2.56E-13 NA
vg0223740729 sf0223734860 2 23740729 NA 4.10E-07
vg0222630367 sf0222624498 2 22630367 NA 1.55E-06
vg0222817468 sf0222811599 2 22817468 NA 2.67E-06