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 mr1069 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
vg0222718166 sf0222712297 2 22718166 7.91E-59 1.95E-34
vg0222725003 sf0222719134 2 22725003 2.17E-19 1.01E-13
vg0113935237 sf0113934211 1 13935237 4.83E-18 NA
vg0800545388 sf0800544388 8 545388 4.74E-17 NA
vg1203613911 sf1203612910 12 3613911 5.07E-17 1.10E-06
vg0524300403 sf0524237822 5 24300403 1.73E-12 NA
vg0311698039 sf0311696757 3 11698039 7.07E-12 5.03E-06
vg0223721789 sf0223715920 2 23721789 NA 3.12E-12
vg0222817468 sf0222811599 2 22817468 NA 8.46E-08
vg0225406731 sf0225400862 2 25406731 NA 4.78E-07
vg0222633031 sf0222627162 2 22633031 NA 1.14E-06
vg0222406943 sf0222401074 2 22406943 NA 1.50E-06
vg0110090809 sf0110089785 1 10090809 NA 1.74E-06
vg0224294117 sf0224288248 2 24294117 NA 2.06E-06
vg0222041029 sf0222035160 2 22041029 NA 2.17E-06
vg1203666075 sf1203665074 12 3666075 NA 2.83E-06
vg0224242820 sf0224236951 2 24242820 NA 4.18E-06
vg0224012738 sf0224006869 2 24012738 NA 4.37E-06
vg0403298006 sf0403293609 4 3298006 NA 4.89E-06
vg1112606104 sf1112142307 11 12606104 NA 4.91E-06