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 mr1006 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
vg0921456056 sf0921455575 9 21456056 7.91E-24 1.12E-18
vg0921374490 sf0921374009 9 21374490 1.13E-13 8.58E-09
vg0910063987 sf0910062986 9 10063987 5.04E-11 4.61E-07
vg0915555915 sf0915554914 9 15555915 9.70E-11 4.05E-06
vg0922446085 sf0922445604 9 22446085 1.75E-10 NA
vg0915182972 sf0915181971 9 15182972 6.40E-07 2.41E-06
vg0520828244 sf0520765685 5 20828244 8.60E-06 3.31E-07