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 mr1308 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
vg1216843164 sf1216837118 12 16843164 3.43E-22 9.95E-06
vg1213458584 sf1213455922 12 13458584 9.78E-22 NA
vg1019985250 sf1019913749 10 19985250 1.89E-21 3.10E-06
vg1020040118 sf1019968616 10 20040118 3.65E-21 2.25E-06
vg0502905717 sf0502905693 5 2905717 6.80E-21 NA
vg0310767670 sf0310766586 3 10767670 8.50E-21 NA
vg0216625646 sf0216619776 2 16625646 3.43E-20 1.74E-07
vg0216625939 sf0216620069 2 16625939 4.15E-20 1.84E-07
vg1212949457 sf1212946796 12 12949457 2.10E-17 9.63E-07
vg1217913079 sf1217884513 12 17913079 NA 7.41E-07
vg0216852215 sf0216846345 2 16852215 NA 1.04E-06
vg1213913884 sf1213911222 12 13913884 NA 3.60E-06
vg0702281324 sf0702280325 7 2281324 NA 4.06E-06