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 mr1314 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
vg0623833223 sf0623832226 6 23833223 4.22E-08 3.75E-07
vg0327981236 sf0327974290 3 27981236 3.08E-07 2.18E-06
vg0406854973 sf0406850418 4 6854973 5.33E-07 7.34E-07
vg0516129069 sf0516071553 5 16129069 NA 2.44E-06
vg0321406609 sf0321405119 3 21406609 NA 2.95E-06
vg0202138774 sf0202138774 2 2138774 NA 3.05E-06
vg0912052073 sf0912051072 9 12052073 NA 4.06E-06