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 mr1081 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
vg0222745001 sf0222739132 2 22745001 1.93E-40 3.22E-10
vg0222732157 sf0222726288 2 22732157 4.42E-40 3.01E-10
vg0917685025 sf0917684024 9 17685025 8.09E-40 NA
vg0626585101 sf0626584104 6 26585101 5.01E-39 NA
vg0914768468 sf0914767467 9 14768468 1.04E-37 NA
vg0705494006 sf0705493007 7 5494006 1.32E-37 NA
vg1202398699 sf1202397700 12 2398699 5.34E-34 NA
vg0130832570 sf0130831526 1 30832570 NA 5.42E-07
vg0222628680 sf0222622811 2 22628680 NA 1.67E-06
vg1122217828 sf1121751699 11 22217828 NA 1.85E-06
vg1122219057 sf1121752928 11 22219057 NA 2.83E-06
vg0601101826 sf0601100827 6 1101826 NA 4.84E-06
vg0406864531 sf0406859976 4 6864531 NA 8.11E-06