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 mr1708 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
vg0424007589 sf0423822447 4 24007589 3.11E-09 1.79E-07
vg0424121172 sf0423936033 4 24121172 5.91E-09 1.24E-07
vg0907769964 sf0907768964 9 7769964 2.03E-07 2.92E-06
vg0724902343 sf0724901349 7 24902343 2.51E-07 1.02E-06
vg0904631897 sf0904630897 9 4631897 9.71E-07 6.42E-06
vg0702641922 sf0702640923 7 2641922 1.27E-06 4.87E-06
vg0113678139 sf0113677113 1 13678139 2.14E-06 2.80E-06
vg1121614615 sf1121148492 11 21614615 3.09E-06 3.17E-06
vg0726930454 sf0726929460 7 26930454 7.09E-06 1.83E-06