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 mr1200 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
vg0610608095 sf0610607096 6 10608095 5.93E-32 4.61E-21
vg0610872773 sf0610871774 6 10872773 9.21E-15 8.55E-09
vg0610871994 sf0610870995 6 10871994 1.81E-12 8.59E-07
vg0610609229 sf0610608230 6 10609229 3.83E-11 6.42E-07
vg0610462486 sf0610461487 6 10462486 8.55E-11 5.81E-09
vg0610435285 sf0610434286 6 10435285 1.98E-10 2.08E-08
vg0610433780 sf0610432781 6 10433780 3.16E-10 1.25E-08
vg0610965158 sf0610964159 6 10965158 5.42E-10 9.75E-06
vg0613057898 sf0613056899 6 13057898 5.75E-09 4.70E-07
vg0610413099 sf0610412100 6 10413099 1.01E-08 7.60E-09
vg0612105145 sf0612104146 6 12105145 1.93E-08 1.73E-06
vg0612016809 sf0612015810 6 12016809 8.67E-08 1.95E-06
vg0610752378 sf0610751379 6 10752378 1.04E-07 1.69E-07
vg0617636450 sf0617635453 6 17636450 3.94E-07 7.89E-07
vg0611643367 sf0611642368 6 11643367 1.81E-06 3.10E-06