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 mr1709 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
vg1003467337 sf1003466314 10 3467337 2.80E-11 2.54E-06
vg1005164651 sf1005181188 10 5164651 1.29E-10 6.79E-07
vg0200713263 sf0200713263 2 713263 3.97E-10 5.36E-06
vg0524300403 sf0524237822 5 24300403 2.38E-09 NA
vg0823416687 sf0823413974 8 23416687 7.37E-08 NA
vg0609547477 sf0609546478 6 9547477 6.80E-06 1.83E-07