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 mr1600 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
vg0222741535 sf0222735666 2 22741535 8.70E-24 3.18E-18
vg0809709071 sf0809708075 8 9709071 8.65E-12 NA
vg0705549134 sf0705548135 7 5549134 1.49E-11 NA
vg0626889330 sf0626888333 6 26889330 2.24E-11 NA
vg0211295378 sf0211295375 2 11295378 2.92E-11 NA
vg0211185461 sf0211185458 2 11185461 2.52E-10 4.00E-06
vg0905265793 sf0905264793 9 5265793 2.31E-09 NA
vg0214182384 sf0214176514 2 14182384 1.10E-08 NA
vg0605513869 sf0605512870 6 5513869 NA 9.43E-07
vg0222725003 sf0222719134 2 22725003 NA 9.91E-07
vg0131880868 sf0131879824 1 31880868 NA 3.32E-06