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 mr1823 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
vg0131567146 sf0131566102 1 31567146 3.14E-08 NA
vg0102103204 sf0102102204 1 2103204 7.20E-08 7.67E-06
vg0805608836 sf0805607839 8 5608836 2.74E-06 4.99E-06
vg1125669886 sf1125203725 11 25669886 2.81E-06 8.90E-06
vg0805992743 sf0805991746 8 5992743 4.35E-06 2.44E-06
vg0706162756 sf0706161757 7 6162756 NA 2.47E-06