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 mr1712 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
vg0419841239 sf0419669276 4 19841239 4.35E-09 2.57E-07
vg0419845324 sf0419673360 4 19845324 5.29E-09 2.59E-07
vg0728114135 sf0728113142 7 28114135 3.75E-08 NA
vg0230036264 sf0230030395 2 30036264 4.98E-08 NA
vg0601102379 sf0601101380 6 1102379 6.18E-08 NA
vg0804887405 sf0804886408 8 4887405 6.24E-08 1.22E-06
vg1217054050 sf1217048004 12 17054050 1.77E-07 1.33E-06
vg0808322645 sf0808321649 8 8322645 3.30E-07 4.11E-06
vg0232030438 sf0232024569 2 32030438 8.38E-07 NA
vg0904077185 sf0904076185 9 4077185 8.52E-07 4.63E-06