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 mr1553 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
vg0323605084 sf0323603258 3 23605084 4.02E-17 NA
vg0141321523 sf0141320480 1 41321523 1.26E-16 NA
vg0130749115 sf0130748071 1 30749115 8.85E-16 NA
vg0134596832 sf0134595789 1 34596832 9.98E-16 NA
vg0111998777 sf0111997751 1 11998777 1.62E-15 NA
vg1203864713 sf1203863712 12 3864713 3.75E-14 NA
vg0425253104 sf0425067966 4 25253104 2.10E-13 6.30E-07
vg1204727738 sf1204726723 12 4727738 NA 2.34E-06
vg1126875179 sf1126403566 11 26875179 NA 7.44E-06