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 mr1759 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
vg0703631746 sf0703630747 7 3631746 1.74E-08 NA
vg1109561136 sf1109555713 11 9561136 3.66E-08 NA
vg0603940269 sf0603939270 6 3940269 4.31E-08 NA
vg0614879232 sf0614878233 6 14879232 6.81E-08 NA
vg0521868263 sf0521805705 5 21868263 6.97E-08 8.35E-06
vg0414193101 sf0414183817 4 14193101 7.89E-08 3.80E-06
vg0409265113 sf0409260386 4 9265113 2.84E-06 3.35E-06
vg1216282575 sf1216279871 12 16282575 NA 8.20E-07