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 mr1102 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
vg1012371707 sf1012300522 10 12371707 1.64E-37 2.82E-06
vg1118815887 sf1118349695 11 18815887 6.82E-36 NA
vg0109404215 sf0109403191 1 9404215 1.44E-35 NA
vg0607100843 sf0607099844 6 7100843 2.09E-35 NA
vg0805820164 sf0805819167 8 5820164 2.21E-35 NA
vg0107647091 sf0107646091 1 7647091 7.59E-33 1.81E-07
vg1012400571 sf1012329386 10 12400571 1.93E-32 NA
vg1115484424 sf1115020737 11 15484424 NA 2.35E-08
vg1115520675 sf1115056988 11 15520675 NA 5.42E-08
vg1201256540 sf1201255540 12 1256540 NA 1.72E-07
vg0132525698 sf0132524654 1 32525698 NA 2.83E-07
vg0523195489 sf0523132930 5 23195489 NA 3.64E-07
vg1124001841 sf1123535711 11 24001841 NA 6.28E-07
vg1221736592 sf1221703139 12 21736592 NA 7.79E-07
vg1215553595 sf1215550892 12 15553595 NA 8.86E-07
vg1115512017 sf1115048330 11 15512017 NA 1.63E-06
vg1208274233 sf1208271639 12 8274233 NA 3.29E-06
vg0818200735 sf0818198022 8 18200735 NA 3.47E-06