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 mr1541 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
vg0217328110 sf0217322240 2 17328110 6.46E-25 1.09E-06
vg0918001087 sf0918000086 9 18001087 4.30E-24 9.38E-06
vg0717067914 sf0717066921 7 17067914 4.91E-23 NA
vg1118876899 sf1118410708 11 18876899 7.07E-23 NA
vg0518537224 sf0518474799 5 18537224 8.22E-23 NA
vg0517394193 sf0517333836 5 17394193 1.52E-20 NA