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 mr1700 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
vg0124420479 sf0124419435 1 24420479 7.00E-07 7.00E-07
vg0138706549 sf0138705506 1 38706549 1.23E-06 1.23E-06
vg1214630257 sf1214627597 12 14630257 1.41E-06 1.41E-06
vg0805005643 sf0805004646 8 5005643 2.04E-06 2.04E-06
vg0805900956 sf0805899959 8 5900956 2.11E-06 2.11E-06
vg0205851172 sf0205851172 2 5851172 3.26E-06 3.26E-06