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 mr1103 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
vg0719011406 sf0719010413 7 19011406 1.82E-30 2.23E-23
vg0717227488 sf0717226495 7 17227488 1.85E-16 1.25E-10
vg1201545939 sf1201544939 12 1545939 7.61E-14 2.64E-06
vg0707706006 sf0707705011 7 7706006 2.05E-13 9.00E-07
vg1201356688 sf1201355688 12 1356688 2.31E-13 2.17E-07
vg0719242112 sf0719241119 7 19242112 2.33E-13 8.67E-07
vg0719003833 sf0719002840 7 19003833 4.15E-11 8.87E-07
vg1201578984 sf1201577984 12 1578984 1.01E-10 1.64E-06
vg0719465974 sf0719464981 7 19465974 2.66E-10 4.42E-09
vg0224293556 sf0224287687 2 24293556 3.55E-10 1.19E-08
vg1214370012 sf1214367353 12 14370012 1.25E-09 1.95E-06
vg0228210940 sf0228205071 2 28210940 5.21E-09 4.09E-07
vg0920282336 sf0920281855 9 20282336 7.93E-09 5.15E-07
vg0721581014 sf0721580021 7 21581014 2.33E-08 NA
vg0431597089 sf0431411984 4 31597089 3.12E-07 2.87E-06
vg0504291251 sf0504291228 5 4291251 6.96E-07 7.32E-07
vg0517802935 sf0517742421 5 17802935 9.63E-07 NA
vg1202552737 sf1202551739 12 2552737 1.12E-06 NA
vg0719192005 sf0719191012 7 19192005 1.74E-06 5.57E-07
vg0226057933 sf0226052064 2 26057933 2.79E-06 3.90E-06
vg0718887161 sf0718886168 7 18887161 2.93E-06 4.39E-07
vg1218153748 sf1218125184 12 18153748 3.04E-06 NA
vg0719451062 sf0719450069 7 19451062 4.44E-06 1.90E-06
vg0718985745 sf0718984752 7 18985745 NA 9.40E-08
vg0211829965 sf0211829961 2 11829965 NA 8.22E-07
vg0235249589 sf0235243720 2 35249589 NA 2.56E-06