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 mr1544 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
vg1214823465 sf1214820806 12 14823465 5.12E-07 5.12E-07
vg1124660528 sf1124194368 11 24660528 9.46E-07 9.46E-07
vg0623833223 sf0623832226 6 23833223 2.84E-06 2.84E-06
vg1016224206 sf1016152978 10 16224206 3.41E-06 3.41E-06
vg1122149845 sf1121683716 11 22149845 3.57E-06 3.57E-06
vg0919745618 sf0919745137 9 19745618 4.00E-06 4.00E-06
vg0513542683 sf0513485230 5 13542683 4.33E-06 4.33E-06
vg0729363250 sf0729362258 7 29363250 8.66E-06 8.66E-06