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 mr1740 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
vg0805565774 sf0805564777 8 5565774 1.60E-09 NA
vg0125037562 sf0125036518 1 25037562 2.70E-09 NA
vg1119923512 sf1119457435 11 19923512 3.09E-09 NA
vg1117484883 sf1117018738 11 17484883 5.51E-09 NA
vg0706195526 sf0706194527 7 6195526 6.67E-09 NA
vg1202795096 sf1202794098 12 2795096 4.58E-08 NA
vg0429750241 sf0429565110 4 29750241 6.35E-06 1.38E-06
vg0603899937 sf0603898938 6 3899937 8.17E-06 NA
vg0321855451 sf0321853961 3 21855451 8.61E-06 1.39E-06