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 mr1110 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
vg0610362020 sf0610361021 6 10362020 8.15E-10 8.15E-10
vg0616129303 sf0616128305 6 16129303 4.76E-08 4.76E-08
vg0610649207 sf0610648208 6 10649207 6.48E-08 6.48E-08
vg1008589261 sf1008518123 10 8589261 1.79E-07 1.79E-07
vg0613223540 sf0613222541 6 13223540 7.54E-07 7.54E-07
vg0105393860 sf0105392860 1 5393860 1.63E-06 1.63E-06
vg1016434902 sf1016363676 10 16434902 2.18E-06 2.18E-06
vg0403922728 sf0403918334 4 3922728 3.67E-06 3.67E-06
vg0720170421 sf0720169428 7 20170421 4.93E-06 4.93E-06