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 mr1703 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
vg0325696417 sf0325694435 3 25696417 4.29E-13 2.69E-11
vg0609926305 sf0609925306 6 9926305 2.96E-08 1.83E-07
vg1010676624 sf1010605445 10 10676624 9.63E-08 NA
vg0400345487 sf0400344487 4 345487 9.66E-08 2.18E-06
vg1107093285 sf1107089030 11 7093285 1.13E-07 3.51E-06
vg1004099607 sf1004238601 10 4099607 1.61E-07 3.51E-06
vg1012753141 sf1012681956 10 12753141 3.67E-07 3.42E-06
vg1123452531 sf1122986401 11 23452531 7.69E-06 NA