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 mr1440 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
vg0922386993 sf0922386512 9 22386993 9.53E-07 9.53E-07
vg1215169176 sf1215166512 12 15169176 1.49E-06 1.49E-06
vg1112750621 sf1112286942 11 12750621 3.12E-06 3.12E-06
vg0621412586 sf0621411589 6 21412586 3.34E-06 3.34E-06
vg0820839590 sf0820836877 8 20839590 4.00E-06 4.00E-06