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 mr1523 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
vg1104990849 sf1104986660 11 4990849 5.22E-09 5.22E-09
vg0119857925 sf0119856880 1 19857925 6.39E-07 6.39E-07
vg0908611714 sf0908610713 9 8611714 7.72E-07 7.72E-07
vg1113860205 sf1113396526 11 13860205 8.45E-07 8.45E-07
vg0119837345 sf0119836300 1 19837345 2.36E-06 2.36E-06
vg1104927782 sf1104923593 11 4927782 2.60E-06 2.60E-06
vg0332073154 sf0332066031 3 32073154 2.89E-06 2.89E-06
vg0714470576 sf0714469583 7 14470576 4.23E-06 4.23E-06