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 mr1817 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
vg0919907956 sf0919907475 9 19907956 3.99E-29 1.12E-06
vg0919907680 sf0919907199 9 19907680 1.00E-28 1.98E-07
vg0725508763 sf0725507769 7 25508763 9.23E-27 NA
vg0131415417 sf0131414373 1 31415417 1.85E-26 NA
vg1007351768 sf1007367391 10 7351768 3.10E-26 NA
vg0801766010 sf0801765013 8 1766010 6.20E-26 NA
vg0920090369 sf0920089888 9 20090369 2.20E-22 5.76E-07
vg1207302951 sf1207300358 12 7302951 NA 2.69E-06
vg0804605906 sf0804604909 8 4605906 NA 3.55E-06
vg1203587545 sf1203586544 12 3587545 NA 3.82E-06
vg1216729892 sf1216723846 12 16729892 NA 3.97E-06