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
vg0921461602 sf0921461121 9 21461602 4.66E-26 1.14E-20
vg0921456056 sf0921455575 9 21456056 7.08E-26 6.27E-22
vg0922446085 sf0922445604 9 22446085 2.06E-10 NA
vg0921456248 sf0921455767 9 21456248 3.35E-10 4.52E-07
vg0915555915 sf0915554914 9 15555915 2.45E-09 3.90E-06
vg0524622529 sf0524559949 5 24622529 7.52E-09 NA
vg0921533165 sf0921532684 9 21533165 5.57E-08 4.98E-10
vg0915107342 sf0915106341 9 15107342 1.76E-07 NA
vg0406758253 sf0406753699 4 6758253 5.17E-07 3.36E-06
vg0620211423 sf0620210426 6 20211423 3.84E-06 3.16E-07
vg1219397316 sf1219368786 12 19397316 5.59E-06 NA
vg0718139747 sf0718138754 7 18139747 NA 4.52E-07
vg0408141959 sf0408137233 4 8141959 NA 3.81E-06
vg0626990911 sf0626989914 6 26990911 NA 4.79E-06