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 mr1079 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
vg1215968758 sf1215966054 12 15968758 4.19E-80 3.72E-34
vg1215854982 sf1215852278 12 15854982 8.31E-75 2.52E-34
vg1209571445 sf1209568854 12 9571445 5.55E-59 1.15E-21
vg1210300519 sf1210297932 12 10300519 1.13E-55 2.16E-26
vg1223872806 sf1223839259 12 23872806 2.57E-46 3.06E-09
vg1223898220 sf1223864673 12 2389822