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 mr1746 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
vg0800287831 sf0800286831 8 287831 1.43E-50 7.31E-25
vg0800284313 sf0800283313 8 284313 2.67E-30 5.68E-16
vg0800202591 sf0800201591 8 202591 2.30E-26 2.43E-17
vg0800063298 sf0800062298 8 63298 3.78E-26 1.21E-17
vg0800160345 sf0800159345 8 160345 1.23E-18 1.52E-06
vg0800430481 sf0800429481 8 430481 6.24E-15 1.25E-09
vg0812659243 sf0812657068 8 12659243 2.65E-14 NA
vg0622302569 sf0622301572 6 22302569 5.20E-12 9.17E-07
vg0409507807 sf0409498505 4 9507807 1.01E-11 5.68E-07
vg0800195356 sf0800194356 8 195356 1.12E-11 6.80E-17
vg0800307583 sf0800306583 8 307583 NA 5.04E-08
vg0817248882 sf0817246168 8 17248882 NA 3.62E-07
vg0817248199 sf0817245485 8 17248199 NA 1.12E-06
vg0800453306 sf0800452306 8 453306 NA 1.75E-06
vg0715227955 sf0715226962 7 15227955 NA 2.11E-06
vg0523735868 sf0523673289 5 23735868 NA 2.44E-06
vg0413108547 sf0413099257 4 13108547 NA 4.09E-06