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 mr1707 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
vg0617988684 sf0617987687 6 17988684 5.98E-09 2.83E-06
vg0617995261 sf0617994264 6 17995261 6.13E-09 2.48E-06
vg1119340990 sf1118874678 11 19340990 1.95E-06 8.07E-07
vg0822641799 sf0822639086 8 22641799 2.31E-06 3.07E-06
vg0719735381 sf0719734388 7 19735381 NA 2.33E-06
vg0605357766 sf0605356767 6 5357766 NA 3.01E-06
vg0702729357 sf0702728358 7 2729357 NA 9.22E-06