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 mr1500 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
vg0224819264 sf0224813395 2 24819264 8.72E-09 4.17E-06
vg0101354617 sf0101353617 1 1354617 6.02E-08 NA
vg0529913786 sf0529851141 5 29913786 1.87E-06 NA
vg0109054780 sf0109053780 1 9054780 6.09E-06 NA
vg0420828431 sf0420656474 4 20828431 6.18E-06 3.70E-06
vg0314925439 sf0314924086 3 14925439 NA 1.71E-06
vg0717153722 sf0717152729 7 17153722 NA 1.87E-06