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
vg0814655004 sf0814652290 8 14655004 1.64E-06 1.64E-06
vg0122790443 sf0122789399 1 22790443 2.16E-06 2.17E-06
vg1001244211 sf1001243188 10 1244211 2.24E-06 2.24E-06
vg0825508271 sf0825505557 8 25508271 2.93E-06 2.94E-06
vg1123190871 sf1122724742 11 23190871 4.41E-06 4.42E-06
vg0329014410 sf0329007462 3 29014410 4.64E-06 4.64E-06