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 mr1984 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
vg1016430707 sf1016359481 10 16430707 2.02E-08 2.02E-08
vg0709448532 sf0709447538 7 9448532 7.39E-08 7.39E-08
vg0819451071 sf0819448358 8 19451071 9.46E-07 9.46E-07
vg0202013925 sf0202013925 2 2013925 1.98E-06 1.98E-06
vg0420664918 sf0420492961 4 20664918 3.68E-06 3.68E-06
vg0141975851 sf0141974808 1 41975851 3.90E-06 3.90E-06