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 mr1606 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
vg0630078359 sf0630077361 6 30078359 3.61E-09 2.27E-08
vg0900499731 sf0900498731 9 499731 6.86E-08 4.40E-06
vg0314751950 sf0314750637 3 14751950 2.96E-07 5.85E-06
vg0335525852 sf0335518721 3 35525852 7.50E-07 3.56E-06
vg0707853841 sf0707852846 7 7853841 9.68E-07 5.19E-07
vg1216729892 sf1216723846 12 16729892 3.08E-06 1.01E-06
vg0401606597 sf0401602146 4 1606597 5.25E-06 NA
vg0908668780 sf0908667779 9 8668780 6.35E-06 5.32E-06
vg0434375933 sf0434190827 4 34375933 8.13E-06 4.47E-06
vg1102446151 sf1102442055 11 2446151 NA 1.92E-06
vg0910546560 sf0910545559 9 10546560 NA 4.61E-06
vg0910719137 sf0910718136 9 10719137 NA 6.50E-06