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 mr1780 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
vg1121911743 sf1121445614 11 21911743 2.70E-09 NA
vg1017929024 sf1017857796 10 17929024 1.17E-08 9.10E-07
vg0722110531 sf0722109538 7 22110531 1.66E-08 NA
vg0719030151 sf0719029158 7 19030151 2.04E-08 NA
vg1017951405 sf1017880177 10 17951405 2.13E-08 7.67E-07
vg1000635609 sf1000634585 10 635609 2.71E-08 NA
vg0216006804 sf0216000934 2 16006804 3.71E-08 NA
vg0611427499 sf0611426500 6 11427499 7.27E-06 NA