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 mr1731 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
vg0427543202 sf0427358063 4 27543202 8.06E-09 NA
vg0428025706 sf0427840570 4 28025706 6.23E-08 NA
vg0700969178 sf0700968178 7 969178 6.78E-08 NA
vg1019294434 sf1019222989 10 19294434 1.67E-07 1.24E-06
vg0807177027 sf0807176032 8 7177027 2.16E-06 4.05E-06
vg0113185147 sf0113184121 1 13185147 2.80E-06 3.27E-06