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 mr1401 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
vg1217054403 sf1217048357 12 17054403 2.48E-19 NA
vg0310800424 sf0310799142 3 10800424 2.94E-19 NA
vg0502333732 sf0502333707 5 2333732 2.01E-18 NA
vg0408205825 sf0408201099 4 8205825 4.65E-18 NA
vg0204450989 sf0204450986 2 4450989 6.10E-18 NA
vg0502242174 sf0502242149 5 2242174 2.80E-16 3.40E-06
vg0817221859 sf0817219145 8 17221859 3.80E-15 3.93E-06
vg0310703455 sf0310702371 3 10703455 NA 3.54E-08
vg0208100222 sf0208100221 2 8100222 NA 2.25E-07
vg0727615010 sf0727614016 7 27615010 NA 2.91E-07
vg0201061873 sf0201061873 2 1061873 NA 2.15E-06
vg0823432095 sf0823429382 8 23432095 NA 2.51E-06
vg1114869807 sf1114406121 11 14869807 NA 3.41E-06
vg0501786396 sf0501786379 5 1786396 NA 3.58E-06
vg0617626072 sf0617625075 6 17626072 NA 6.62E-06