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 mr1340 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
vg1107376701 sf1107372446 11 7376701 3.13E-08 3.14E-08
vg0224868229 sf0224862360 2 24868229 8.25E-08 8.28E-08
vg0420600418 sf0420428462 4 20600418 3.85E-07 3.86E-07
vg0804126025 sf0804125028 8 4126025 8.59E-07 8.62E-07
vg0621261248 sf0621260251 6 21261248 9.70E-07 9.68E-07
vg0327302530 sf0327295583 3 27302530 1.11E-06 1.11E-06
vg0515257168 sf0515199710 5 15257168 1.75E-06 1.75E-06
vg1222744855 sf1222711294 12 22744855 3.02E-06 3.03E-06
vg1218075103 sf1218046539 12 18075103 3.17E-06 3.18E-06
vg1218471759 sf1218443195 12 18471759 3.23E-06 3.25E-06
vg0319031415 sf0319030175 3 19031415 3.69E-06 3.70E-06