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 mr1122 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
vg0306613252 sf0306612252 3 6613252 5.44E-07 5.45E-07
vg0209141112 sf0209141110 2 9141112 5.71E-07 5.71E-07
vg0130865887 sf0130864843 1 30865887 9.42E-07 9.42E-07
vg0921387658 sf0921387177 9 21387658 2.05E-06 2.06E-06
vg0721028689 sf0721027696 7 21028689 2.18E-06 2.18E-06
vg0706378896 sf0706377901 7 6378896 2.37E-06 2.37E-06
vg0901718260 sf0901717260 9 1718260 2.93E-06 2.93E-06
vg0204541828 sf0204541825 2 4541828 3.08E-06 3.09E-06
vg0805393123 sf0805392126 8 5393123 4.43E-06 4.44E-06
vg1220284744 sf1220256186 12 20284744 4.75E-06 4.75E-06
vg0103525065 sf0103524065 1 3525065 4.79E-06 4.79E-06