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 mr1222 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
vg0316592255 sf0316590900 3 16592255 1.38E-08 NA
vg0805066201 sf0805065204 8 5066201 2.23E-08 9.03E-06
vg0307967118 sf0307966056 3 7967118 5.28E-08 NA
vg0805063346 sf0805062349 8 5063346 5.75E-08 8.81E-06
vg1017965103 sf1017893875 10 17965103 2.20E-07 1.90E-06