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 mr1909 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
vg0205284721 sf0205284719 2 5284721 5.46E-38 3.10E-17
vg0205285315 sf0205285313 2 5285315 2.04E-36 4.88E-18
vg0132981784 sf0132980740 1 32981784 9.46E-21 NA
vg0208287625 sf0208287624 2 8287625 3.88E-20 NA
vg0138520632 sf0138519589 1 38520632 4.12E-20 NA
vg1111009061 sf1111003378 11 11009061 4.45E-19 NA
vg1109493114 sf1109487691 11 9493114 7.84E-14 NA
vg0205293173 sf0205293171 2 5293173 NA 6.23E-11
vg1207088649 sf1207087539 12 7088649 NA 1.46E-06
vg0205279787 sf0205279784 2 5279787 NA 2.10E-06
vg1215653812 sf1215651109 12 15653812 NA 3.76E-06