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 mr1352 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
vg1210634977 sf1210632390 12 10634977 3.44E-11 5.04E-06
vg1210133928 sf1210131339 12 10133928 1.95E-10 2.21E-07
vg0500663400 sf0500663400 5 663400 5.81E-10 NA
vg0729558870 sf0729557878 7 29558870 1.36E-09 NA
vg0803291998 sf0803291001 8 3291998 2.12E-09 NA
vg0431920149 sf0431735044 4 31920149 3.45E-09 NA
vg1217331200 sf1217325155 12 17331200 6.28E-09 9.21E-07
vg0423891208 sf0423706066 4 23891208 1.39E-08 1.09E-06
vg0504371369 sf0504371346 5 4371369 3.16E-08 9.43E-08
vg0912516801 sf0912515800 9 12516801 6.77E-07 NA
vg0800148454 sf0800147454 8 148454 4.28E-06 NA
vg1014032310 sf1013961076 10 14032310 6.07E-06 7.59E-06