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 mr1430 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
vg0315007040 sf0315005687 3 15007040 9.73E-07 9.73E-07
vg1002827884 sf1002826861 10 2827884 1.03E-06 1.03E-06
vg0415427207 sf0415417892 4 15427207 1.47E-06 1.47E-06
vg0314656096 sf0314654783 3 14656096 2.80E-06 2.80E-06
vg0314967098 sf0314965745 3 14967098 3.57E-06 3.57E-06