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 mr1600 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
vg0211185461 sf0211185458 2 11185461 5.33E-07 1.76E-07
vg0822330414 sf0822327701 8 22330414 6.26E-07 4.44E-06
vg0421349976 sf0421178030 4 21349976 3.34E-06 NA
vg0605513869 sf0605512870 6 5513869 5.47E-06 8.82E-07
vg0810533736 sf0810532740 8 10533736 NA 1.67E-06
vg0316243138 sf0316241786 3 16243138 NA 1.70E-06
vg1216567539 sf1216564832 12 16567539 NA 1.92E-06