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 mr1436 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
vg0719011406 sf0719010413 7 19011406 5.29E-40 1.63E-10
vg0719049906 sf0719048913 7 19049906 1.70E-35 2.41E-19
vg0305273043 sf0305272043 3 5273043 2.09E-35 8.35E-06
vg0917077829 sf0917076828 9 17077829 4.57E-34 NA
vg0708204553 sf0708203558 7 8204553 1.85E-33 NA
vg0215989562 sf0215983692 2 15989562 3.34E-33 NA
vg0719091461 sf0719090468 7 19091461 NA 4.07E-14
vg0718865378 sf0718864385 7 18865378 NA 1.13E-10
vg0719067465 sf0719066472 7 19067465 NA 2.14E-09
vg0719132485 sf0719131492 7 19132485 NA 7.52E-09
vg0428494128 sf0428308982 4 28494128 NA 1.64E-08
vg0901040131 sf0901039131 9 1040131 NA 1.31E-07
vg0329561125 sf0329554165 3 29561125 NA 6.92E-07
vg0719060385 sf0719059392 7 19060385 NA 1.13E-06
vg0616957969 sf0616956972 6 16957969 NA 1.27E-06
vg0609456504 sf0609455505 6 9456504 NA 1.40E-06
vg0617438772 sf0617437775 6 17438772 NA 2.49E-06
vg1109089203 sf1109083816 11 9089203 NA 2.74E-06
vg0719466615 sf0719465622 7 19466615 NA 3.02E-06
vg1009704100 sf1009632921 10 9704100 NA 3.48E-06
vg0801055392 sf0801054394 8 1055392 NA 3.49E-06
vg0714471636 sf0714470643 7 14471636 NA 3.60E-06
vg1207833484 sf1207830890 12 7833484 NA 6.88E-06