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 mr1081 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
vg0222722732 sf0222716863 2 22722732 3.58E-09 3.58E-09
vg0222716046 sf0222710177 2 22716046 4.88E-09 4.88E-09
vg0710985476 sf0710984482 7 10985476 1.38E-06 1.38E-06
vg0200460907 sf0200460907 2 460907 1.76E-06 1.76E-06
vg1214822308 sf1214819649 12 14822308 2.20E-06 2.20E-06
vg0224283930 sf0224278061 2 24283930 2.45E-06 2.45E-06
vg0229918162 sf0229912293 2 29918162 2.55E-06 2.55E-06
vg0816201029 sf0816198315 8 16201029 2.62E-06 2.62E-06
vg0223168818 sf0223162949 2 23168818 2.89E-06 2.89E-06
vg1210166479 sf1210163890 12 10166479 3.05E-06 3.05E-06
vg0816756907 sf0816754193 8 16756907 3.33E-06 3.33E-06
vg0421031231 sf0420859284 4 21031231 3.42E-06 3.42E-06