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 mr1008 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
vg0133471381 sf0133470337 1 33471381 1.91E-184 1.56E-49
vg0133595311 sf0133594267 1 33595311 9.97E-184 2.05E-52
vg0130140335 sf0130139290 1 30140335 1.85E-126 2.38E-06
vg0902245657 sf0902244657 9 2245657 4.02E-120 NA
vg0137243519 sf0137242476 1 37243519 1.99E-116 NA
vg0326760318 sf0326753372 3 26760318 2.89E-114 NA
vg0133497043 sf0133495999 1 33497043 NA 2.25E-10
vg0133704031 sf0133702987 1 33704031 NA 5.98E-09
vg0133722922 sf0133721878 1 33722922 NA 1.14E-08
vg0230014670 sf0230008801 2 30014670 NA 6.57E-08
vg0900588490 sf0900587490 9 588490 NA 1.19E-07
vg0604220066 sf0604219067 6 4220066 NA 3.09E-07
vg0133259170 sf0133258126 1 33259170 NA 3.97E-07
vg0921541460 sf0921540979 9 21541460 NA 4.40E-07
vg0133639693 sf0133638649 1 33639693 NA 5.62E-07
vg0921455943 sf0921455462 9 21455943 NA 6.45E-07
vg0211188937 sf0211188934 2 11188937 NA 7.72E-07
vg0900534728 sf0900533728 9 534728 NA 9.44E-07
vg0921567751 sf0921567270 9 21567751 NA 1.18E-06
vg0135170016 sf0135168973 1 35170016 NA 1.91E-06
vg0401159831 sf0401155381 4 1159831 NA 2.45E-06
vg0123535121 sf0123534077 1 23535121 NA 2.55E-06
vg0704462910 sf0704461911 7 4462910 NA 2.81E-06
vg0722755496 sf0722754503 7 22755496 NA 2.96E-06
vg0707066814 sf0707065819 7 7066814 NA 3.11E-06
vg0707363161 sf0707362166 7 7363161 NA 7.97E-06