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 mr1706 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
vg0205285714 sf0205285712 2 5285714 1.97E-11 2.43E-07
vg0205292054 sf0205292052 2 5292054 3.64E-11 1.47E-07
vg0141763299 sf0141762256 1 41763299 2.35E-09 NA
vg0141821909 sf0141820866 1 41821909 2.40E-09 NA
vg0105521069 sf0105520069 1 5521069 3.23E-09 NA
vg0726964336 sf0726963342 7 26964336 5.01E-09 NA
vg1222399385 sf1222365824 12 22399385 2.94E-08 7.18E-06
vg0727110534 sf0727109540 7 27110534 4.26E-07 4.26E-06
vg0221240541 sf0221234673 2 21240541 4.97E-07 2.46E-06
vg0122969231 sf0122968187 1 22969231 2.25E-06 NA
vg0524187250 sf0524124669 5 24187250 4.62E-06 NA
vg0232481318 sf0232475449 2 32481318 9.85E-06 1.47E-06
vg1214656787 sf1214654127 12 14656787 NA 1.04E-06
vg0425304166 sf0425119028 4 25304166 NA 4.50E-06