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
vg0303440042 sf0303439038 3 3440042 7.98E-29 NA
vg0116074965 sf0116073939 1 16074965 4.64E-28 NA
vg0428045444 sf0427860309 4 28045444 8.79E-28 NA
vg0917282150 sf0917281149 9 17282150 1.14E-27 NA
vg0607115256 sf0607114257 6 7115256 1.64E-27 NA
vg0116188975 sf0116187949 1 16188975 9.23E-26 NA
vg0800302779 sf0800301779 8 302779 NA 4.40E-07
vg1214666563 sf1214663903 12 14666563 NA 1.58E-06
vg0519456069 sf0519393553 5 19456069 NA 2.35E-06
vg1019294434 sf1019222989 10 19294434 NA 5.36E-06