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 mr1051 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
vg0921459327 sf0921458846 9 21459327 2.02E-14 8.69E-11
vg0921537073 sf0921536592 9 21537073 6.17E-14 2.97E-12
vg0915456404 sf0915455403 9 15456404 1.51E-11 NA
vg0205319588 sf0205319587 2 5319588 3.88E-09 NA
vg0133648958 sf0133647914 1 33648958 5.98E-09 1.83E-07
vg0922398401 sf0922397920 9 22398401 2.20E-08 NA
vg0133772134 sf0133771090 1 33772134 4.37E-07 1.37E-06
vg0133305513 sf0133304469 1 33305513 5.70E-07 4.27E-06
vg1217056602 sf1217050557 12 17056602 6.02E-07 4.35E-06
vg0608564755 sf0608563756 6 8564755 3.31E-06 1.62E-06
vg1215993370 sf1215990666 12 15993370 5.13E-06 NA
vg0112515893 sf0112514867 1 12515893 NA 2.39E-06