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 mr1730 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
vg0405860613 sf0405856054 4 5860613 7.71E-08 4.89E-06
vg0324646650 sf0324644729 3 24646650 3.39E-07 NA
vg1009049826 sf1008978687 10 9049826 3.85E-07 1.66E-07
vg0111122073 sf0111121049 1 11122073 1.62E-06 5.63E-07
vg0721129130 sf0721128137 7 21129130 2.18E-06 1.43E-06
vg0512875775 sf0512818697 5 12875775 5.10E-06 NA
vg0313175610 sf0313174531 3 13175610 6.79E-06 NA
vg0810948653 sf0810947658 8 10948653 NA 4.49E-06