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 mr1229 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
vg1117596580 sf1117130437 11 17596580 5.10E-09 5.79E-06
vg0617039640 sf0617038643 6 17039640 1.60E-06 6.41E-06
vg0202217757 sf0202217757 2 2217757 1.87E-06 4.71E-07
vg0114209645 sf0114208619 1 14209645 1.96E-06 1.14E-06
vg1205242056 sf1205241042 12 5242056 2.62E-06 3.59E-06
vg0125113438 sf0125112394 1 25113438 3.27E-06 NA
vg0522542822 sf0522480264 5 22542822 9.90E-06 NA
vg1117151190 sf1116685042 11 17151190 NA 5.51E-06