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 mr1979 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
vg0420711795 sf0420539838 4 20711795 5.92E-07 5.92E-07
vg1005078467 sf1005095004 10 5078467 1.43E-06 1.43E-06
vg0223522349 sf0223516480 2 23522349 2.78E-06 2.78E-06
vg0130239724 sf0130238679 1 30239724 2.89E-06 2.89E-06
vg1002271573 sf1002270550 10 2271573 2.93E-06 2.93E-06
vg0122971925 sf0122970881 1 22971925 3.47E-06 3.47E-06
vg0403552516 sf0403548118 4 3552516 4.46E-06 4.47E-06
vg0825542549 sf0825539835 8 25542549 5.00E-06 5.00E-06