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 mr1546 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
vg1215968355 sf1215965651 12 15968355 5.42E-45 7.69E-09
vg1215981440 sf1215978736 12 15981440 1.57E-43 3.69E-10
vg1210130934 sf1210128345 12 10130934 8.01E-42 7.74E-07
vg1209691528 sf1209688937 12 9691528 3.03E-39 1.96E-07
vg1223872806 sf1223839259 12 23872806 1.12E-36 NA
vg1017670851 sf1017599624 10 17670851 1.31E-36 1.00E-07
vg0216310015 sf0216304145 2 16310015 2.37E-35 NA
vg1216993314 sf1216987268 12 16993314 NA 6.68E-09
vg1209218924 sf1209216333 12 9218924 NA 4.74E-08
vg1216058319 sf1216055615 12 16058319 NA 6.05E-07
vg1214119279 sf1214116619 12 14119279 NA 7.97E-07
vg0402252227 sf0402247822 4 2252227 NA 1.21E-06
vg0915834013 sf0915833012 9 15834013 NA 2.57E-06
vg0208731146 sf0208731145 2 8731146 NA 3.98E-06