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 mr1002 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
vg1207888547 sf1207885953 12 7888547 4.89E-19 3.28E-10
vg0907965825 sf0907964825 9 7965825 1.05E-13 6.62E-06
vg0727505200 sf0727504206 7 27505200 1.57E-13 NA
vg0119284442 sf0119283397 1 19284442 2.03E-13 NA
vg0803869823 sf0803868826 8 3869823 2.22E-11 NA
vg0806189701 sf0806188706 8 6189701 7.05E-08 1.23E-06