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 mr1015 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
vg0133688513 sf0133687469 1 33688513 3.02E-14 5.17E-13
vg0217651623 sf0217645753 2 17651623 8.94E-11 3.67E-06
vg0500580717 sf0500580717 5 580717 4.84E-10 NA
vg0142148398 sf0142147354 1 42148398 1.27E-09 6.29E-06
vg0131506032 sf0131504988 1 31506032 2.65E-09 NA
vg0133643942 sf0133642898 1 33643942 5.06E-09 3.19E-07
vg0406790251 sf0406785696 4 6790251 6.90E-08 NA
vg0142054143 sf0142053100 1 42054143 1.90E-06 3.86E-06
vg0628005554 sf0628004556 6 28005554 8.31E-06 NA
vg0135567772 sf0135566729 1 35567772 NA 3.08E-06
vg0122343655 sf0122342610 1 22343655 NA 3.32E-06