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 mr1307 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
vg1016429449 sf1016358223 10 16429449 5.95E-08 5.95E-08
vg0628528239 sf0628527241 6 28528239 2.60E-06 2.60E-06
vg1007900043 sf1007915653 10 7900043 2.79E-06 2.79E-06
vg0726962702 sf0726961708 7 26962702 2.95E-06 2.95E-06
vg0500206143 sf0500206143 5 206143 3.66E-06 3.67E-06