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 mr1729 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
vg1119923512 sf1119457435 11 19923512 6.77E-11 NA
vg1210647989 sf1210645402 12 10647989 7.68E-11 NA
vg1210993634 sf1210991000 12 10993634 4.17E-10 4.79E-06
vg1100795910 sf1100794911 11 795910 6.14E-10 NA
vg0500814826 sf0500814808 5 814826 1.40E-09 NA
vg0218472132 sf0218466263 2 18472132 1.43E-09 NA
vg1010255814 sf1010184635 10 10255814 1.39E-07 7.49E-07
vg1218796192 sf1218767627 12 18796192 2.21E-07 NA
vg0804864010 sf0804863013 8 4864010 7.10E-07 1.60E-06
vg0804865671 sf0804864674 8 4865671 8.90E-07 2.00E-06
vg0328933796 sf0328926848 3 28933796 1.74E-06 3.99E-06
vg0314622952 sf0314621639 3 14622952 NA 1.40E-06
vg0314987126 sf0314985773 3 14987126 NA 2.18E-06
vg0212831487 sf0212831483 2 12831487 NA 2.49E-06
vg0728386754 sf0728385762 7 28386754 NA 3.75E-06