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 mr1112 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
vg0611239376 sf0611238377 6 11239376 6.60E-07 6.60E-07
vg0610118958 sf0610117959 6 10118958 1.36E-06 1.36E-06
vg0311072594 sf0311071312 3 11072594 3.36E-06 3.36E-06
vg0616129303 sf0616128305 6 16129303 3.87E-06 3.87E-06
vg0115667573 sf0115666547 1 15667573 9.15E-06 9.14E-06