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 mr1510 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
vg0501159328 sf0501159312 5 1159328 9.34E-09 NA
vg0501385926 sf0501385910 5 1385926 7.40E-08 5.54E-06
vg0500179859 sf0500179859 5 179859 1.39E-07 6.67E-06
vg0715810096 sf0715809103 7 15810096 1.85E-06 6.45E-07
vg0719154234 sf0719153241 7 19154234 3.41E-06 1.00E-06