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 mr1020 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
vg0224678499 sf0224672630 2 24678499 2.62E-07 5.23E-07
vg1013323230 sf1013251999 10 13323230 2.06E-06 3.77E-06
vg0824007713 sf0824004999 8 24007713 2.24E-06 NA
vg0617714472 sf0617713475 6 17714472 2.75E-06 7.19E-07
vg1002941211 sf1002940188 10 2941211 5.48E-06 NA
vg0906665147 sf0906664147 9 6665147 NA 3.30E-06